diff --git a/CHANGELOG.md b/CHANGELOG.md index efba3ecf..0cf182dc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ - Numerous changes to column names in viral hits TSV, mainly to improve clarity - Updated mislabeled processes - Added instructions for what to do should you run out of API requests for containers +- Unzipped gold standard reference output in `test-data/gold-standard-results` # v2.7.0.2 - Updated `pipeline-version.txt` diff --git a/test-data/gold-standard-results/bracken_reports_merged.tsv b/test-data/gold-standard-results/bracken_reports_merged.tsv new file mode 100644 index 00000000..0ffd0319 --- /dev/null +++ b/test-data/gold-standard-results/bracken_reports_merged.tsv @@ -0,0 +1,3 @@ +name taxid rank kraken_assigned_reads added_reads new_est_reads fraction_total_reads sample ribosomal +Viruses 10239 D 1 0 1 1.00000 gold_standard TRUE +Viruses 10239 D 41 0 41 1.00000 gold_standard FALSE diff --git a/test-data/gold-standard-results/bracken_reports_merged.tsv.gz b/test-data/gold-standard-results/bracken_reports_merged.tsv.gz deleted file mode 100644 index 73853322..00000000 Binary files a/test-data/gold-standard-results/bracken_reports_merged.tsv.gz and /dev/null differ diff --git a/test-data/gold-standard-results/kraken_reports_merged.tsv b/test-data/gold-standard-results/kraken_reports_merged.tsv new file mode 100644 index 00000000..149df85c --- /dev/null +++ b/test-data/gold-standard-results/kraken_reports_merged.tsv @@ -0,0 +1,78 @@ +pc_reads_total n_reads_clade n_reads_direct n_minimizers_total n_minimizers_distinct rank taxid name sample ribosomal +95.65 22 22 0 0 U 0 unclassified gold_standard TRUE +4.35 1 0 21 4 R 1 root gold_standard TRUE +4.35 1 0 21 4 D 10239 Viruses gold_standard TRUE +4.35 1 0 4 3 D1 2559587 Riboviria gold_standard TRUE +4.35 1 0 4 3 K 2732396 Orthornavirae gold_standard TRUE +4.35 1 0 4 3 P 2497569 Negarnaviricota gold_standard TRUE +4.35 1 0 4 3 P1 2497571 Polyploviricotina gold_standard TRUE +4.35 1 0 4 3 C 2497576 Ellioviricetes gold_standard TRUE +4.35 1 0 4 3 O 1980410 Bunyavirales gold_standard TRUE +4.35 1 0 4 3 F 1980416 Peribunyaviridae gold_standard TRUE +4.35 1 0 4 3 G 11572 Orthobunyavirus gold_standard TRUE +4.35 1 0 4 3 S 3052437 Orthobunyavirus schmallenbergense gold_standard TRUE +4.35 1 1 4 3 S1 159150 Shamonda virus gold_standard TRUE +33.87 21 21 0 0 U 0 unclassified gold_standard FALSE +66.13 41 0 1001 986 R 1 root gold_standard FALSE +66.13 41 0 1001 986 D 10239 Viruses gold_standard FALSE +61.29 38 0 990 977 D1 2559587 Riboviria gold_standard FALSE +61.29 38 0 989 976 K 2732396 Orthornavirae gold_standard FALSE +32.26 20 0 747 737 P 2732406 Kitrinoviricota gold_standard FALSE +20.97 13 0 616 616 C 2732461 Alsuviricetes gold_standard FALSE +20.97 13 0 616 616 O 2732544 Martellivirales gold_standard FALSE +20.97 13 0 616 616 F 675071 Virgaviridae gold_standard FALSE +20.97 13 0 616 616 G 12234 Tobamovirus gold_standard FALSE +9.68 6 6 279 279 S 12239 Pepper mild mottle virus gold_standard FALSE +4.84 3 3 173 173 S 12235 Cucumber green mottle mosaic virus gold_standard FALSE +3.23 2 2 79 79 S 12241 Tobacco mild green mosaic virus gold_standard FALSE +1.61 1 1 45 45 S 12242 Tobacco mosaic virus gold_standard FALSE +1.61 1 1 30 30 S 12253 Tomato mosaic virus gold_standard FALSE +11.29 7 0 131 121 C 2732463 Tolucaviricetes gold_standard FALSE +11.29 7 0 131 121 O 2732548 Tolivirales gold_standard FALSE +11.29 7 0 131 121 F 39738 Tombusviridae gold_standard FALSE +11.29 7 0 131 121 F1 2560077 Procedovirinae gold_standard FALSE +11.29 7 0 131 121 G 1911601 Gammacarmovirus gold_standard FALSE +11.29 7 0 131 121 S 3048200 Gammacarmovirus melonis gold_standard FALSE +11.29 7 7 131 121 S1 11987 Melon necrotic spot virus gold_standard FALSE +27.42 17 0 240 237 P 2732408 Pisuviricota gold_standard FALSE +16.13 10 0 136 136 C 2732507 Stelpaviricetes gold_standard FALSE +16.13 10 0 136 136 O 2732551 Stellavirales gold_standard FALSE +16.13 10 0 136 136 F 39733 Astroviridae gold_standard FALSE +9.68 6 0 55 55 G 249588 Mamastrovirus gold_standard FALSE +4.84 3 3 25 25 S 1239565 Mamastrovirus 1 gold_standard FALSE +3.23 2 0 24 24 S 1239570 Mamastrovirus 6 gold_standard FALSE +3.23 2 2 24 24 S1 568715 Astrovirus MLB1 gold_standard FALSE +1.61 1 0 6 6 G1 526119 unclassified Mamastrovirus gold_standard FALSE +1.61 1 1 5 5 S 1389204 Feline astrovirus 2 gold_standard FALSE +6.45 4 0 67 67 F1 352926 unclassified Astroviridae gold_standard FALSE +6.45 4 4 66 66 S 1868658 Human astrovirus gold_standard FALSE +11.29 7 0 103 100 C 2732506 Pisoniviricetes gold_standard FALSE +11.29 7 0 103 100 O 464095 Picornavirales gold_standard FALSE +6.45 4 0 64 64 F 12058 Picornaviridae gold_standard FALSE +4.84 3 0 56 56 F1 2946635 Kodimesavirinae gold_standard FALSE +4.84 3 0 56 56 G 194960 Kobuvirus gold_standard FALSE +4.84 3 0 55 55 S 72149 Kobuvirus aichi gold_standard FALSE +4.84 3 3 55 55 S1 1313215 aichivirus A1 gold_standard FALSE +1.61 1 0 4 4 F1 2946640 Paavivirinae gold_standard FALSE +1.61 1 0 4 4 G 138954 Parechovirus gold_standard FALSE +1.61 1 0 4 4 S 1803956 Parechovirus A gold_standard FALSE +1.61 1 1 2 2 S1 12063 parechovirus A1 gold_standard FALSE +4.84 3 0 39 36 F 232795 Dicistroviridae gold_standard FALSE +4.84 3 0 39 36 F1 336635 unclassified Dicistroviridae gold_standard FALSE +4.84 3 3 39 36 S 1776109 Goose dicistrovirus gold_standard FALSE +1.61 1 0 2 2 P 2732405 Duplornaviricota gold_standard FALSE +1.61 1 0 2 2 C 2732459 Resentoviricetes gold_standard FALSE +1.61 1 0 2 2 O 2732541 Reovirales gold_standard FALSE +1.61 1 0 2 2 F 2946186 Sedoreoviridae gold_standard FALSE +1.61 1 0 2 2 G 10912 Rotavirus gold_standard FALSE +1.61 1 1 2 2 S 28875 Rotavirus A gold_standard FALSE +4.84 3 0 10 8 D1 2732004 Varidnaviria gold_standard FALSE +4.84 3 0 10 8 K 2732005 Bamfordvirae gold_standard FALSE +4.84 3 0 10 8 P 2732007 Nucleocytoviricota gold_standard FALSE +4.84 3 0 10 8 C 2732525 Pokkesviricetes gold_standard FALSE +4.84 3 0 10 8 O 2732527 Chitovirales gold_standard FALSE +4.84 3 0 10 8 F 10240 Poxviridae gold_standard FALSE +4.84 3 0 10 8 F1 10241 Chordopoxvirinae gold_standard FALSE +4.84 3 0 10 8 G 2733297 Oryzopoxvirus gold_standard FALSE +4.84 3 0 10 8 G1 2788403 unclassified Oryzopoxvirus gold_standard FALSE +4.84 3 3 10 8 S 67082 BeAn 58058 virus gold_standard FALSE diff --git a/test-data/gold-standard-results/kraken_reports_merged.tsv.gz b/test-data/gold-standard-results/kraken_reports_merged.tsv.gz deleted file mode 100644 index b0fe1786..00000000 Binary files a/test-data/gold-standard-results/kraken_reports_merged.tsv.gz and /dev/null differ diff --git a/test-data/gold-standard-results/merged_blast_filtered.tsv b/test-data/gold-standard-results/merged_blast_filtered.tsv new file mode 100644 index 00000000..d012a1b5 --- /dev/null +++ b/test-data/gold-standard-results/merged_blast_filtered.tsv @@ -0,0 +1,31 @@ +qseqid sseqid sgi staxid qlen evalue bitscore qcovs length pident mismatch gapopen sstrand qstart qend sstart send bitscore_rank_dense bitscore_fraction +SRR12204734.102846486 gi|1799084385|gb|MN030571.1| 1799084385 2699435 141 9.47e-30 134 100 141 83.688 23 0 minus 1 141 3990 3850 1 1.0 +SRR12204734.102846486 gi|2571040051|gb|OR130732.1| 2571040051 3071813 141 9.47e-30 134 100 141 83.688 23 0 minus 1 141 3990 3850 2 1.0 +SRR12204734.132645528 gi|2510069797|gb|ON398705.1| 2510069797 3049538 128 2.89e-59 231 100 128 99.219 1 0 minus 1 128 4697 4570 1 1.0 +SRR12204734.136705306 gi|1799084385|gb|MN030571.1| 1799084385 2699435 140 1.53e-47 193 98 137 91.971 11 0 minus 4 140 1036 900 1 1.0 +SRR12204734.136705306 gi|2571040051|gb|OR130732.1| 2571040051 3071813 140 1.53e-47 193 98 137 91.971 11 0 minus 4 140 1036 900 2 1.0 +SRR12204734.146348965 gi|1799084385|gb|MN030571.1| 1799084385 2699435 142 7.38e-31 137 71 101 92.079 3 1 minus 1 101 6359 6264 1 1.0 +SRR12204734.146348965 gi|2571040051|gb|OR130732.1| 2571040051 3071813 142 7.38e-31 137 71 101 92.079 3 1 minus 1 101 6760 6665 2 1.0 +SRR12204734.146348965 gi|1430400470|gb|MF927778.1| 1430400470 2268895 142 2.69e-20 102 72 102 85.294 11 2 minus 1 102 9379 9282 2 0.7445255474452555 +SRR12204734.158389317 gi|1799084385|gb|MN030571.1| 1799084385 2699435 140 1.95e-56 222 99 138 95.652 6 0 minus 1 138 1669 1532 1 1.0 +SRR12204734.158389317 gi|2571040051|gb|OR130732.1| 2571040051 3071813 140 1.95e-56 222 99 138 95.652 6 0 minus 1 138 1669 1532 2 1.0 +SRR12204848.140127907 gi|1799084385|gb|MN030571.1| 1799084385 2699435 143 1.58e-42 176 100 143 88.811 16 0 minus 1 143 1854 1712 1 1.0 +SRR12204848.140127907 gi|2571040051|gb|OR130732.1| 2571040051 3071813 143 1.58e-42 176 100 143 88.811 16 0 minus 1 143 1854 1712 2 1.0 +SRR12204848.15085913 gi|1799084385|gb|MN030571.1| 1799084385 2699435 142 2.04e-36 156 72 103 94.175 4 2 plus 41 142 1938 2039 1 1.0 +SRR12204848.15085913 gi|2571040051|gb|OR130732.1| 2571040051 3071813 142 2.04e-36 156 72 103 94.175 4 2 plus 41 142 1938 2039 2 1.0 +SRR12204848.28156033 gi|1799084385|gb|MN030571.1| 1799084385 2699435 136 1.90e-46 189 99 135 91.852 11 0 plus 1 135 1633 1767 1 1.0 +SRR12204848.28156033 gi|2571040051|gb|OR130732.1| 2571040051 3071813 136 1.90e-46 189 99 135 91.852 11 0 plus 1 135 1633 1767 2 1.0 +SRR12204848.31434798 gi|1799084385|gb|MN030571.1| 1799084385 2699435 147 4.47e-53 211 100 147 92.517 11 0 plus 1 147 1180 1326 1 1.0 +SRR12204848.31434798 gi|2571040051|gb|OR130732.1| 2571040051 3071813 147 4.47e-53 211 100 147 92.517 11 0 plus 1 147 1180 1326 2 1.0 +SRR12204849.140297134 gi|2510069797|gb|ON398705.1| 2510069797 3049538 148 5.71e-67 257 100 148 97.973 3 0 plus 1 148 2798 2945 1 1.0 +SRR12204849.142401718 gi|2294264610|gb|MW678777.1| 2294264610 32630 144 9.31e-60 233 100 144 95.833 6 0 minus 1 144 2225 2082 1 1.0 +SRR12204849.142401718 gi|2571040051|gb|OR130732.1| 2571040051 3071813 144 4.33e-58 228 100 144 95.139 7 0 minus 1 144 5510 5367 2 0.9785407725321889 +SRR12204849.147306033 gi|2450664545|dbj|LC723624.1| 2450664545 2973485 146 4.37e-63 244 99 144 97.222 4 0 plus 3 146 499 642 1 1.0 +SRR12204849.16071359 gi|2784409127|gb|PQ072823.1| 2784409127 32630 138 1.51e-42 176 99 139 89.928 10 3 plus 1 137 63 199 1 1.0 +SRR12204850.120094795 gi|380719094|gb|JQ281544.1| 380719094 1163660 148 1.24e-63 246 100 148 96.622 5 0 minus 1 148 646 499 1 1.0 +SRR12204850.140730292 gi|1799084385|gb|MN030571.1| 1799084385 2699435 139 1.16e-53 213 100 139 94.245 8 0 plus 1 139 2108 2246 1 1.0 +SRR12204850.140730292 gi|2571040051|gb|OR130732.1| 2571040051 3071813 139 1.16e-53 213 100 139 94.245 8 0 plus 1 139 2108 2246 2 1.0 +SRR12204850.28709236 gi|380719094|gb|JQ281544.1| 380719094 1163660 148 3.51e-49 198 95 140 92.143 11 0 plus 3 142 4290 4429 1 1.0 +SRR12204850.8190301 gi|380719094|gb|JQ281544.1| 380719094 1163660 147 2.69e-50 202 99 145 91.724 12 0 minus 1 145 5481 5337 1 1.0 +SRR12204850.89255206 gi|1799084385|gb|MN030571.1| 1799084385 2699435 148 4.51e-53 211 99 147 92.517 11 0 minus 2 148 553 407 1 1.0 +SRR12204850.89255206 gi|2571040051|gb|OR130732.1| 2571040051 3071813 148 4.51e-53 211 99 147 92.517 11 0 minus 2 148 553 407 2 1.0 diff --git a/test-data/gold-standard-results/merged_blast_filtered.tsv.gz b/test-data/gold-standard-results/merged_blast_filtered.tsv.gz deleted file mode 100644 index 957bda37..00000000 Binary files a/test-data/gold-standard-results/merged_blast_filtered.tsv.gz and /dev/null differ diff --git a/test-data/gold-standard-results/read_counts.tsv b/test-data/gold-standard-results/read_counts.tsv new file mode 100644 index 00000000..3a0daacf --- /dev/null +++ b/test-data/gold-standard-results/read_counts.tsv @@ -0,0 +1,2 @@ +sample n_reads_single n_read_pairs +gold_standard 330 165 diff --git a/test-data/gold-standard-results/read_counts.tsv.gz b/test-data/gold-standard-results/read_counts.tsv.gz deleted file mode 100644 index eacfb360..00000000 Binary files a/test-data/gold-standard-results/read_counts.tsv.gz and /dev/null differ diff --git a/test-data/gold-standard-results/subset_qc_adapter_stats.tsv b/test-data/gold-standard-results/subset_qc_adapter_stats.tsv new file mode 100644 index 00000000..dc529ce6 --- /dev/null +++ b/test-data/gold-standard-results/subset_qc_adapter_stats.tsv @@ -0,0 +1,109 @@ +position pc_adapters file adapter stage sample +1 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +2 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +3 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +4 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +5 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +6 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +7 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +8 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +9 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +12 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +17 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +22 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +27 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +32 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +37 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +42 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +47 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +52 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +57 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +62 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +67 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +72 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +77 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +82 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +87 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +92 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +97 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +102 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +107 0 gold_standard_interleaved illumina_universal_adapter raw gold_standard +112 1.1428571428571428 gold_standard_interleaved illumina_universal_adapter raw gold_standard +117 4.571428571428571 gold_standard_interleaved illumina_universal_adapter raw gold_standard +122 5.714285714285714 gold_standard_interleaved illumina_universal_adapter raw gold_standard +127 5.714285714285714 gold_standard_interleaved illumina_universal_adapter raw gold_standard +132 8.38095238095238 gold_standard_interleaved illumina_universal_adapter raw gold_standard +137 10.857142857142858 gold_standard_interleaved illumina_universal_adapter raw gold_standard +140 12.380952380952381 gold_standard_interleaved illumina_universal_adapter raw gold_standard +1 0 gold_standard_interleaved polya raw gold_standard +2 0 gold_standard_interleaved polya raw gold_standard +3 0 gold_standard_interleaved polya raw gold_standard +4 0 gold_standard_interleaved polya raw gold_standard +5 0 gold_standard_interleaved polya raw gold_standard +6 0 gold_standard_interleaved polya raw gold_standard +7 0 gold_standard_interleaved polya raw gold_standard +8 0 gold_standard_interleaved polya raw gold_standard +9 0 gold_standard_interleaved polya raw gold_standard +12 0.38095238095238093 gold_standard_interleaved polya raw gold_standard +17 0.8571428571428571 gold_standard_interleaved polya raw gold_standard +22 1.0476190476190477 gold_standard_interleaved polya raw gold_standard +27 1.4285714285714286 gold_standard_interleaved polya raw gold_standard +32 1.8095238095238095 gold_standard_interleaved polya raw gold_standard +37 1.9047619047619047 gold_standard_interleaved polya raw gold_standard +42 2.0952380952380953 gold_standard_interleaved polya raw gold_standard +47 2.380952380952381 gold_standard_interleaved polya raw gold_standard +52 2.380952380952381 gold_standard_interleaved polya raw gold_standard +57 2.380952380952381 gold_standard_interleaved polya raw gold_standard +62 2.380952380952381 gold_standard_interleaved polya raw gold_standard +67 2.380952380952381 gold_standard_interleaved polya raw gold_standard +72 2.666666666666667 gold_standard_interleaved polya raw gold_standard +77 2.857142857142857 gold_standard_interleaved polya raw gold_standard +82 2.857142857142857 gold_standard_interleaved polya raw gold_standard +87 2.857142857142857 gold_standard_interleaved polya raw gold_standard +92 2.857142857142857 gold_standard_interleaved polya raw gold_standard +97 2.857142857142857 gold_standard_interleaved polya raw gold_standard +102 2.857142857142857 gold_standard_interleaved polya raw gold_standard +107 2.857142857142857 gold_standard_interleaved polya raw gold_standard +112 2.857142857142857 gold_standard_interleaved polya raw gold_standard +117 2.857142857142857 gold_standard_interleaved polya raw gold_standard +122 2.857142857142857 gold_standard_interleaved polya raw gold_standard +127 2.857142857142857 gold_standard_interleaved polya raw gold_standard +132 2.857142857142857 gold_standard_interleaved polya raw gold_standard +137 2.857142857142857 gold_standard_interleaved polya raw gold_standard +140 2.857142857142857 gold_standard_interleaved polya raw gold_standard +1 1.4285714285714286 gold_standard_interleaved polyg raw gold_standard +2 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +3 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +4 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +5 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +6 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +7 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +8 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +9 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +12 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +17 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +22 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +27 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +32 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +37 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +42 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +47 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +52 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +57 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +62 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +67 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +72 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +77 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +82 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +87 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +92 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +97 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +102 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +107 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +112 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +117 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +122 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +127 1.9047619047619047 gold_standard_interleaved polyg raw gold_standard +132 2.2857142857142856 gold_standard_interleaved polyg raw gold_standard +137 2.380952380952381 gold_standard_interleaved polyg raw gold_standard +140 2.380952380952381 gold_standard_interleaved polyg raw gold_standard diff --git a/test-data/gold-standard-results/subset_qc_adapter_stats.tsv.gz b/test-data/gold-standard-results/subset_qc_adapter_stats.tsv.gz deleted file mode 100644 index d7c98a62..00000000 Binary files a/test-data/gold-standard-results/subset_qc_adapter_stats.tsv.gz and /dev/null differ diff --git a/test-data/gold-standard-results/subset_qc_basic_stats.tsv b/test-data/gold-standard-results/subset_qc_basic_stats.tsv new file mode 100644 index 00000000..b60aec9c --- /dev/null +++ b/test-data/gold-standard-results/subset_qc_basic_stats.tsv @@ -0,0 +1,3 @@ +percent_gc mean_seq_len n_reads_single n_read_pairs percent_duplicates n_bases_approx per_base_sequence_quality per_sequence_quality_scores per_base_sequence_content per_sequence_gc_content per_base_n_content sequence_length_distribution sequence_duplication_levels overrepresented_sequences adapter_content stage sample +46 150.24761904761905 210 105 4.285714285714278 31500 pass pass fail fail pass warn pass fail fail raw gold_standard +47 145.31764705882352 170 85 7.058823529411768 24700 pass pass fail fail pass warn pass fail pass cleaned gold_standard diff --git a/test-data/gold-standard-results/subset_qc_basic_stats.tsv.gz b/test-data/gold-standard-results/subset_qc_basic_stats.tsv.gz deleted file mode 100644 index 548c2f13..00000000 Binary files a/test-data/gold-standard-results/subset_qc_basic_stats.tsv.gz and /dev/null differ diff --git a/test-data/gold-standard-results/subset_qc_length_stats.tsv b/test-data/gold-standard-results/subset_qc_length_stats.tsv new file mode 100644 index 00000000..5d447a32 --- /dev/null +++ b/test-data/gold-standard-results/subset_qc_length_stats.tsv @@ -0,0 +1,43 @@ +length n_sequences file stage sample +150 158 gold_standard_interleaved raw gold_standard +151 52 gold_standard_interleaved raw gold_standard +112 6 gold_standard_fastp cleaned gold_standard +113 0 gold_standard_fastp cleaned gold_standard +114 0 gold_standard_fastp cleaned gold_standard +115 2 gold_standard_fastp cleaned gold_standard +116 2 gold_standard_fastp cleaned gold_standard +117 2 gold_standard_fastp cleaned gold_standard +118 0 gold_standard_fastp cleaned gold_standard +119 0 gold_standard_fastp cleaned gold_standard +120 0 gold_standard_fastp cleaned gold_standard +121 1 gold_standard_fastp cleaned gold_standard +122 0 gold_standard_fastp cleaned gold_standard +123 0 gold_standard_fastp cleaned gold_standard +124 0 gold_standard_fastp cleaned gold_standard +125 0 gold_standard_fastp cleaned gold_standard +126 0 gold_standard_fastp cleaned gold_standard +127 0 gold_standard_fastp cleaned gold_standard +128 0 gold_standard_fastp cleaned gold_standard +129 4 gold_standard_fastp cleaned gold_standard +130 1 gold_standard_fastp cleaned gold_standard +131 0 gold_standard_fastp cleaned gold_standard +132 0 gold_standard_fastp cleaned gold_standard +133 0 gold_standard_fastp cleaned gold_standard +134 0 gold_standard_fastp cleaned gold_standard +135 2 gold_standard_fastp cleaned gold_standard +136 4 gold_standard_fastp cleaned gold_standard +137 2 gold_standard_fastp cleaned gold_standard +138 0 gold_standard_fastp cleaned gold_standard +139 2 gold_standard_fastp cleaned gold_standard +140 4 gold_standard_fastp cleaned gold_standard +141 4 gold_standard_fastp cleaned gold_standard +142 4 gold_standard_fastp cleaned gold_standard +143 2 gold_standard_fastp cleaned gold_standard +144 2 gold_standard_fastp cleaned gold_standard +145 1 gold_standard_fastp cleaned gold_standard +146 0 gold_standard_fastp cleaned gold_standard +147 1 gold_standard_fastp cleaned gold_standard +148 0 gold_standard_fastp cleaned gold_standard +149 0 gold_standard_fastp cleaned gold_standard +150 79 gold_standard_fastp cleaned gold_standard +151 45 gold_standard_fastp cleaned gold_standard diff --git a/test-data/gold-standard-results/subset_qc_length_stats.tsv.gz b/test-data/gold-standard-results/subset_qc_length_stats.tsv.gz deleted file mode 100644 index c08544f3..00000000 Binary files a/test-data/gold-standard-results/subset_qc_length_stats.tsv.gz and /dev/null differ diff --git a/test-data/gold-standard-results/subset_qc_quality_base_stats.tsv b/test-data/gold-standard-results/subset_qc_quality_base_stats.tsv new file mode 100644 index 00000000..77ea08a7 --- /dev/null +++ b/test-data/gold-standard-results/subset_qc_quality_base_stats.tsv @@ -0,0 +1,77 @@ +position mean_phred_score file stage sample +1 33.39047619047619 gold_standard_interleaved raw gold_standard +2 32.91904761904762 gold_standard_interleaved raw gold_standard +3 34.10476190476191 gold_standard_interleaved raw gold_standard +4 34.80952380952381 gold_standard_interleaved raw gold_standard +5 34.56190476190476 gold_standard_interleaved raw gold_standard +6 36.06190476190476 gold_standard_interleaved raw gold_standard +7 35.84285714285714 gold_standard_interleaved raw gold_standard +8 34.804761904761904 gold_standard_interleaved raw gold_standard +9 35.58571428571429 gold_standard_interleaved raw gold_standard +12 35.266666666666666 gold_standard_interleaved raw gold_standard +17 34.97619047619048 gold_standard_interleaved raw gold_standard +22 34.66571428571429 gold_standard_interleaved raw gold_standard +27 34.80761904761905 gold_standard_interleaved raw gold_standard +32 34.59809523809524 gold_standard_interleaved raw gold_standard +37 34.80571428571429 gold_standard_interleaved raw gold_standard +42 34.81333333333334 gold_standard_interleaved raw gold_standard +47 34.20666666666666 gold_standard_interleaved raw gold_standard +52 34.27047619047619 gold_standard_interleaved raw gold_standard +57 34.359047619047615 gold_standard_interleaved raw gold_standard +62 34.20761904761905 gold_standard_interleaved raw gold_standard +67 34.18571428571429 gold_standard_interleaved raw gold_standard +72 33.986666666666665 gold_standard_interleaved raw gold_standard +77 34.2552380952381 gold_standard_interleaved raw gold_standard +82 34.25333333333334 gold_standard_interleaved raw gold_standard +87 34.16190476190476 gold_standard_interleaved raw gold_standard +92 33.894285714285715 gold_standard_interleaved raw gold_standard +97 34.1447619047619 gold_standard_interleaved raw gold_standard +102 34.0352380952381 gold_standard_interleaved raw gold_standard +107 34.01619047619048 gold_standard_interleaved raw gold_standard +112 33.71142857142858 gold_standard_interleaved raw gold_standard +117 34.01714285714286 gold_standard_interleaved raw gold_standard +122 34.03809523809524 gold_standard_interleaved raw gold_standard +127 33.72190476190476 gold_standard_interleaved raw gold_standard +132 33.597142857142856 gold_standard_interleaved raw gold_standard +137 33.59142857142857 gold_standard_interleaved raw gold_standard +142 33.45047619047619 gold_standard_interleaved raw gold_standard +147 33.289523809523814 gold_standard_interleaved raw gold_standard +150 29.86474358974359 gold_standard_interleaved raw gold_standard +1 34.16470588235294 gold_standard_fastp cleaned gold_standard +2 34.03529411764706 gold_standard_fastp cleaned gold_standard +3 35.00588235294118 gold_standard_fastp cleaned gold_standard +4 35.970588235294116 gold_standard_fastp cleaned gold_standard +5 35.76470588235294 gold_standard_fastp cleaned gold_standard +6 37.258823529411764 gold_standard_fastp cleaned gold_standard +7 36.98235294117647 gold_standard_fastp cleaned gold_standard +8 36.588235294117645 gold_standard_fastp cleaned gold_standard +9 37.294117647058826 gold_standard_fastp cleaned gold_standard +12 36.737647058823534 gold_standard_fastp cleaned gold_standard +17 36.72 gold_standard_fastp cleaned gold_standard +22 36.30705882352941 gold_standard_fastp cleaned gold_standard +27 36.21058823529412 gold_standard_fastp cleaned gold_standard +32 36.423529411764704 gold_standard_fastp cleaned gold_standard +37 36.31058823529412 gold_standard_fastp cleaned gold_standard +42 36.21529411764706 gold_standard_fastp cleaned gold_standard +47 35.65647058823529 gold_standard_fastp cleaned gold_standard +52 35.80588235294117 gold_standard_fastp cleaned gold_standard +57 35.65176470588235 gold_standard_fastp cleaned gold_standard +62 35.76705882352941 gold_standard_fastp cleaned gold_standard +67 35.512941176470584 gold_standard_fastp cleaned gold_standard +72 35.45529411764706 gold_standard_fastp cleaned gold_standard +77 35.511764705882356 gold_standard_fastp cleaned gold_standard +82 35.83529411764706 gold_standard_fastp cleaned gold_standard +87 35.628235294117644 gold_standard_fastp cleaned gold_standard +92 35.35411764705882 gold_standard_fastp cleaned gold_standard +97 35.69411764705882 gold_standard_fastp cleaned gold_standard +102 35.46 gold_standard_fastp cleaned gold_standard +107 35.32352941176471 gold_standard_fastp cleaned gold_standard +112 35.2574175035868 gold_standard_fastp cleaned gold_standard +117 35.36279730255108 gold_standard_fastp cleaned gold_standard +122 35.22118842215593 gold_standard_fastp cleaned gold_standard +127 35.04713375796179 gold_standard_fastp cleaned gold_standard +132 34.982791537667694 gold_standard_fastp cleaned gold_standard +137 34.84032087639189 gold_standard_fastp cleaned gold_standard +142 34.218702482306774 gold_standard_fastp cleaned gold_standard +147 34.23558341013825 gold_standard_fastp cleaned gold_standard +150 30.611648745519716 gold_standard_fastp cleaned gold_standard diff --git a/test-data/gold-standard-results/subset_qc_quality_base_stats.tsv.gz b/test-data/gold-standard-results/subset_qc_quality_base_stats.tsv.gz deleted file mode 100644 index a7bd9b01..00000000 Binary files a/test-data/gold-standard-results/subset_qc_quality_base_stats.tsv.gz and /dev/null differ diff --git a/test-data/gold-standard-results/subset_qc_quality_sequence_stats.tsv b/test-data/gold-standard-results/subset_qc_quality_sequence_stats.tsv new file mode 100644 index 00000000..d63a802b --- /dev/null +++ b/test-data/gold-standard-results/subset_qc_quality_sequence_stats.tsv @@ -0,0 +1,44 @@ +mean_phred_score n_sequences file stage sample +14 2 gold_standard_interleaved raw gold_standard +15 0 gold_standard_interleaved raw gold_standard +16 0 gold_standard_interleaved raw gold_standard +17 0 gold_standard_interleaved raw gold_standard +18 0 gold_standard_interleaved raw gold_standard +19 1 gold_standard_interleaved raw gold_standard +20 1 gold_standard_interleaved raw gold_standard +21 2 gold_standard_interleaved raw gold_standard +22 1 gold_standard_interleaved raw gold_standard +23 7 gold_standard_interleaved raw gold_standard +24 3 gold_standard_interleaved raw gold_standard +25 3 gold_standard_interleaved raw gold_standard +26 2 gold_standard_interleaved raw gold_standard +27 1 gold_standard_interleaved raw gold_standard +28 4 gold_standard_interleaved raw gold_standard +29 5 gold_standard_interleaved raw gold_standard +30 4 gold_standard_interleaved raw gold_standard +31 7 gold_standard_interleaved raw gold_standard +32 11 gold_standard_interleaved raw gold_standard +33 10 gold_standard_interleaved raw gold_standard +34 13 gold_standard_interleaved raw gold_standard +35 16 gold_standard_interleaved raw gold_standard +36 89 gold_standard_interleaved raw gold_standard +37 12 gold_standard_interleaved raw gold_standard +38 6 gold_standard_interleaved raw gold_standard +39 5 gold_standard_interleaved raw gold_standard +40 5 gold_standard_interleaved raw gold_standard +25 1 gold_standard_fastp cleaned gold_standard +26 0 gold_standard_fastp cleaned gold_standard +27 2 gold_standard_fastp cleaned gold_standard +28 1 gold_standard_fastp cleaned gold_standard +29 5 gold_standard_fastp cleaned gold_standard +30 5 gold_standard_fastp cleaned gold_standard +31 6 gold_standard_fastp cleaned gold_standard +32 7 gold_standard_fastp cleaned gold_standard +33 7 gold_standard_fastp cleaned gold_standard +34 11 gold_standard_fastp cleaned gold_standard +35 17 gold_standard_fastp cleaned gold_standard +36 77 gold_standard_fastp cleaned gold_standard +37 14 gold_standard_fastp cleaned gold_standard +38 7 gold_standard_fastp cleaned gold_standard +39 5 gold_standard_fastp cleaned gold_standard +40 5 gold_standard_fastp cleaned gold_standard diff --git a/test-data/gold-standard-results/subset_qc_quality_sequence_stats.tsv.gz b/test-data/gold-standard-results/subset_qc_quality_sequence_stats.tsv.gz deleted file mode 100644 index 7c40eddc..00000000 Binary files a/test-data/gold-standard-results/subset_qc_quality_sequence_stats.tsv.gz and /dev/null differ diff --git a/test-data/gold-standard-results/virus_hits_filtered.tsv b/test-data/gold-standard-results/virus_hits_filtered.tsv new file mode 100644 index 00000000..8cc91bee --- /dev/null +++ b/test-data/gold-standard-results/virus_hits_filtered.tsv @@ -0,0 +1,38 @@ +seq_id bowtie2_genome_id_best bowtie2_genome_id_all bowtie2_taxid_best bowtie2_taxid_all bowtie2_fragment_length bowtie2_genome_id_fwd bowtie2_genome_id_rev bowtie2_taxid_fwd bowtie2_taxid_rev bowtie2_fragment_length_fwd bowtie2_fragment_length_rev bowtie2_best_alignment_score_fwd bowtie2_best_alignment_score_rev bowtie2_next_alignment_score_fwd bowtie2_next_alignment_score_rev bowtie2_edit_distance_fwd bowtie2_edit_distance_rev bowtie2_ref_start_fwd bowtie2_ref_start_rev bowtie2_map_qual_fwd bowtie2_map_qual_rev bowtie2_cigar_fwd bowtie2_cigar_rev query_len_fwd query_len_rev query_seq_fwd query_seq_rev query_qual_fwd query_qual_rev bowtie2_length_normalized_score_fwd bowtie2_length_normalized_score_rev bowtie2_length_normalized_score_max bowtie2_pair_status kraken_classified kraken_assigned_name kraken_assigned_taxid kraken_assigned_host_virus kraken_length kraken_encoded_hits bbmerge_frag_length sample +SRR12204734.102846486 NC_001943.1 NC_001943.1 1868658 1868658 370 NC_001943.1 NC_001943.1 1868658 1868658 370 370 121 146 45 14 17 16 3915 3672 12 12 21S120M 7S101M1D3M1I26M5S 141 143 AATGGGCCGAACAAGGATCTCTGGAAGACTTATGACACCGTAGTCTATGGAGATGATAGGCTCTCCACCACACCTTCAGTGCCAGACAATTATGAAGAAAGAGTAATTGCCATGTATAGAGACATCTTTGGCATGTGGGTT ATTTAGGCACATTAAAGAGATTAGATGGAATTTCATAAACAAAGACCAACGTGAAAAATACAGACATGTGCATGAATGGTATGTTGACAACCTCCTCAATCGTCATGTCTTATTACCATCTGGTGAGGTAACCGTGCAAACAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF FF:FFFFFFFFFFFF:FFFFFFF:FFFF:FFFFFFFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:F,F 24.45056997718949 29.418611880330797 29.418611880330797 CP False unclassified 0 0 285 0:107 A:34 0:51 1239565:5 0:54 NA gold_standard +SRR12204734.122670570 NC_007574.1 NC_007574.1 36427 36427 479 NC_007574.1 NC_007574.1 36427 36427 479 479 162 162 24 10 19 17 353 19 17 17 145M 136M5S 145 141 TACATATTATAAAGATAATGAATTTGTTGTTAGTGATGAATTTTGGTTACATACTAATATAAATGAGTTAATACCATATAAGTTACTATATTATGAACGGGGATTGAGAAAATTATATGATGGTAAAGAGTACATATTGTATAAT GCAATGCGTTCATTATAATTCCGTTCACGGGTGTAAGGAGGGTATTGGGGCTTTTTGAACGCGGGAATCACTTGAATTTTGCAGACACCTACGTATATACGTGGAATCAACAGTATTCATACCATGAGAATGCATTATTAA F:FFFF:FFFF,FFFFF,FFFFFF:FFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF,F:FF,F:,FFFFFF,FFFFFFFFFFFFFFF:FF,FFFFFF,FFFFFFFFFFFFFFFFFF::FF:FFF:F:F:FFFF,F FFF,F:FF:FF,,F,F,F,FF,FFFF,,,FFFFFF,,FF::F,F,FFFFF,FF,F:F,:FFFF,FF,FFFFFFFFF:,FF:F:FFF:FFF,F,,,FF,,FFFFFFFFFFFFFF,,:F:FFFFFFF,FFFFFF,,FF,FFFF 32.55147017794984 32.73547385375783 32.73547385375783 CP False unclassified 0 0 287 0:111 A:34 0:108 NA gold_standard +SRR12204734.132645528 NC_019028.1 NC_019028.1 1247114 1247114 458 NC_019028.1 NC_019028.1 1247114 1247114 458 458 76 15 221 14 12 1 4598 4358 2 2 29S80M19S 119S10M13S 128 142 ATGCTGCCTCTCCAGCCCTTGCTACACTCACACAACATAAAGATGACAGTGAGACCACAAAAACACTTGCAATTAGTTCTGATGGTGCTAATGAACCAGTTGAGATGCTAATACCTGTGAATGAATGG TATGTAGGCTCAATTTGCTAGAAGTCAGACATCAGCCTTTGGTGTTCAACTCAGCTGTGAGTGGTACTGAATCTCGTGTAAGTCTTAACAAGACTACTGGTCCCACTCTAAATTCATGTTCTGGACTTGCAGCTCTAATTCA FFFFFFFFFF,FFF:FFF:FFFFFFFFFFFFFFFFFFFFFF,FFFF:F:FFFFFFFF:F,:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF,:FFFFFFFFFFFFFFF:FFF FF:F,F,:FFFFF,::F,:,FF,F,,FF:F:::FF,F:,,,FFF,:FF:FFFF:FF:FFFFFFFFFFF:,F,:FF,,FF,:FFFF::FFF,FF,:FFFFF:FFFFFF,F,:FFF,FFF,F,FFF,F::F:FFFF:,FFF,FF 15.663546158223031 3.0267400023560063 15.663546158223031 CP True Astrovirus MLB1 568715 1 271 568715:9 0:9 568715:3 0:52 568715:1 0:6 568715:3 0:2 568715:3 0:6 A:34 0:109 NA gold_standard +SRR12204734.136705306 NC_001943.1 NC_001943.1 1868658 1868658 264 NC_001943.1 NC_001943.1 1868658 1868658 264 264 191 199 217 16 12 10 899 784 18 18 137M3S 9S134M3S 140 146 TTACACTTGCAACATCCCATTTGTCTGGTTTTAGGATGGCTGTTTTACCCACAATTCCATTCCACACCACTATGACTTTGTGGGTTATGAACATGCTTATGGTTTGCTACTACTTTGACAATTTGTTATCAATAACAATG CCTAGGGCACATTGGTTAAGAACTGTTTTCTATTACATCCATTATTATGAGATGTGGAATATTTTTATGTTTGTTCTTGCAATTGGCACTGTCATGAGAAGCGCCCGCCCCGGCACAGACTTGATTACACTTGCAACATCCCATTT FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF FFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF 38.65111711161559 39.93092053718007 39.93092053718007 CP True Mamastrovirus 1 1239565 1 264 0:45 1239565:5 0:3 1239565:39 0:8 39733:1 0:4 1239565:1 0:5 1239565:3 0:3 1239565:5 0:1 1239565:8 0:6 1239565:7 0:28 1868658:1 0:5 1239565:1 0:5 1868658:5 0:10 1239565:8 0:23 264 gold_standard +SRR12204734.146348965 NC_022249.1 NC_022249.1 1389204 1389204 242 NC_022249.1 NC_022249.1 1389204 1389204 242 242 140 16 152 14 7 0 6677 6617 2 2 47S37M1D3M4I1M1I49M 91S8M44S 142 143 ATCAAGCACGCAAAGTAGGCGATAATCATGACCTACAAGCTTCAGGAAGCCGCGGCCACGCCGAGTAGGATCGAGGGTACAGCTTCCTTTTCTTCTTTTCTGTCTCTGTTTAGATTATTTTAATCAACATTTAAAATTGATT TTACTTTGAGATGCTTACTTCTCTGCCACAGGCCGGGGCAGCACAATTTGACCAAAGTGAACAAGCAGTAACATTTCATGATAGCCCTGAACAAGCACGATTAAGTGCTGAAGAGACAGATAGTGACTTCGAGAGTACTGAGG FFFFFF:FFFFFFFFF:F:FFFFF,FF:FFFF:FFFFFFF::FF:FFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F,FFFFFFFFF:FFFFFFFF,:FF,,FFFFFFFFFFFFFFFFF,F ::FFFFFF:FFFFFF,FF,FFFFFFFFF::FFFF:,FFFFFFFFFF,FF,FFFFFF:FF:FFFFFFFFFFF,FF:FF,::FF,F:,FFFFFFFFF::,,,:FFFFFFFFFFFF,FF,FFF:FFFF:FFF:F:FFFFFFF,FFF 28.249573355322724 3.2239574663376214 28.249573355322724 CP True Feline astrovirus 2 1389204 1 286 1389204:15 39733:2 1868658:3 0:33 39733:6 2732408:5 1141625:2 0:42 A:34 0:110 NA gold_standard +SRR12204734.158389317 NC_001943.1 NC_001943.1 1868658 1868658 410 NC_001943.1 NC_001943.1 1868658 1868658 410 410 220 113 210 18 8 24 1531 1259 14 14 2S138M 126M8S 140 134 TTCGGTACATGCCCGAAAAGGATATAGCATTCATAACTTGCCCTGGTGATTTGCATCCAACAGCAAGACTAAAATTATCAAAGAATCCAGATTATAGTTGTGTAACAGTTATGGCTTATGTGAATGAAGATCTTGTGGTT GTGATGCTAATGGGAAGTTTGTTGCCACTGTACCAACTATTATCAAAAATGTTGCATTTGAATTCTTACAGAAGCTTAAAAAGTCAGTTGTGAGATTTTTAGTCAATGAGTTTGTAGTTATAAAACAATTTGCT FFF,:FFFFFFFF,,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF:,FFFFFFFFF,FFFFFFFFFFFFFFFFFF,FFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFF:,FFFFFFFFFFFFFFFFFFF ,FF,:F:F::FF:,F:F,FFF::FF,F,FF:F,:FF,FF,,:F,::::,FFFF:::FFF,F,FF:F:F:,F,FFFF,:FF:,FF,::,FFF:FFF,,F,,F,,FFF:FF,FFF::F:FFFFF:F,,FFF,FF:: 44.51961133275095 23.071395679608088 44.51961133275095 CP True Human astrovirus 1868658 1 275 0:1 1239565:1 0:16 1868658:1 0:35 1868658:5 0:34 1868658:2 0:5 39733:1 0:5 A:34 0:58 1239565:5 0:38 NA gold_standard +SRR12204734.194975304 NC_035475.1 NC_035475.1 2021738 2021738 240 NC_035475.1 NC_035475.1 2021738 2021738 240 240 97 133 20 21 15 9 924 996 12 12 24S101M6S 2S95M49S 131 146 ATGTTGCTCTTGAGCCATGTCATTCTGTTCCTGCGCTTGAGGATGAGGAAGCCCTGGTAGTGTGGAGTGCCGTTCTCACCCACTTCCTGCTGCACTATGAGGTATTCAAGGTGCTCCCTCTGCTCATCGTT CTATGAGGTATTCAAGGTGCTCCCTCTGCTCATCGTTCTCCCAGAACTTGTCTTCGTCTTTAGGGTTGTTGATGGTGAAGCACAACCGCTTTGCTGCTCCTTCTGCAACTGGCATCGTGTCGTTCATTCAGATAAAGAATTAGGAT FFFF:FFFFFFFFF,FF:FFFFFFFFF:::FFFFFFFFFFFFFFFFFFF,FFFFFFF:,FFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF F,,F,FF,FFFF,F,:FFFF:,,FF,,F:FF,F,FFFF,FFFF:FF,FFFFF,FF:FFF,:FF:F,F,F,FFFFFFFF::FF,,FFFF::FFF,FFFFFFFF,FFF,F,F:FFFF::F,FFFF:,FFFF,::,FFFFFF,FFFFF: 19.89663055039337 26.687499655502258 26.687499655502258 CP False unclassified 0 0 240 0:140 2021738:5 0:61 240 gold_standard +SRR12204735.74874701 NC_029052.1 NC_029052.1 1776109 1776109 408 NC_029052.1 NC_029052.1 1776109 1776109 408 408 235 233 None 19 8 7 5619 5357 18 18 1S145M 1S141M 146 142 CTAGATAACAAACAAAAAGTTTGTTTGCTCAATACAATGAGTTTTGACAAACATGTTTCTCCAGTTGTTTATGGTGATGATAACATATTAAATGTAAGTGATTATATTAGTGATGTTTTCAATCAGCAAACTTTAACAGATGCGTT AAATACTCAAGTATTATGGTTAGTTTATGAGATTATTGAAAATTTCTACAAGCAGTATGACAAGAATTATAGTGATAAGGATGCAAAGATTCGTTATTCATTGTGGCTCCATATAGTGAATTCAATTCATGTTTATGGAGAT FFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFF:FFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF FFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF 47.15460465445888 47.01536136992996 47.15460465445888 CP True Goose dicistrovirus 1776109 1 289 0:1 1776109:1 0:24 1776109:4 0:15 1776109:5 0:33 1776109:5 0:2 1776109:3 0:13 1776109:6 A:34 0:24 1776109:2 0:9 1776109:4 0:7 1776109:1 0:1 1776109:2 0:35 1776109:1 0:11 1776109:1 0:11 NA gold_standard +SRR12204847.194714938 NC_001943.1 NC_001943.1 1868658 1868658 453 NC_001943.1 NC_001943.1 1868658 1868658 453 453 17 138 16 144 1 20 5091 4661 2 2 124S12M11S 136M1S 147 137 ATTGGCTAGTCAAAGGTGGATGGGGGTTTGTCAAGCTGATTGCAGGTAGAACAAGGAATGGTACGCGTAGCTTCTATGTGTATCCAAGCTACCAGGATGCGCTGTCTAATAAGCCAGCTCTTTGCACTGGAGGGCTTCCAAGTGGGC GTGGAACAACCGAGATTGAGGCGTGTATTCTCCTCAATCCGGTACTTGTTAAGGATGCTACAGGGAGTACTCAATTTGGACCAGTGCAGGCGCTAGGGGCGCAGTATTCAATGTGGAAGCTGAAGTATCTTAATGTG F,F,FF:FFFF::FFFFFFFFFF,:FFFFFFFF,:F:FF:FFFFFFFFFFFFFFFFFF,,F:FFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFF,FFF,F,FFFFF:FFFFFFFFFF:FFFFFFFF:FFFFF:FFFFF::FFF:F F,:,F:FFF::FFFFFFFF::FF,:FFFFFF,,FFF:FFFF:FFFFFF,FFFF,FFFF,,:FF:F:F,,FFFF:,:FFFF:,FF:FFF::FFF,FFFFFFF:FFFF::FFFF:F:FF::F:FFF,:F:,FF:::FF, 3.4065183136705377 28.048889229539444 28.048889229539444 CP False unclassified 0 0 285 0:113 A:34 0:104 NA gold_standard +SRR12204848.140127907 NC_030922.1 NC_030922.1 1239565 1239565 170 NC_030922.1 NC_030922.1 1239565 1239565 170 170 230 219 14 149 8 9 1626 1599 18 18 143M 141M 143 141 GCAGTTCGCACCCAAGATGGGATGTCGGGTGCACCAGTTTGTGACAAGTATGGTCGAGTATTGGCAGTTCATCAAACGAATACTGGATATACCGGAGGGGCTGTTATAATAGATCCAGCAGATTTCCATCCAGTGAAAGCCCC ATTGTACATGGCAACACCCTCTCATATGCAGTTCGCACCCAAGATGGGATGTCGGGTGCACCAGTTTGTGACAAGTATGGTCGAGTATTGGCAGTTCATCAAACGAATACTGGATATACCGGAGGGGCTGTTATAATAGAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF 46.34438857860331 44.2535109504504 46.34438857860331 CP True Mamastrovirus 1 1239565 1 170 0:2 1239565:2 0:51 1239565:1 0:18 1239565:1 0:7 1239565:2 0:16 1239565:3 0:1 1239565:5 0:11 1239565:5 0:5 1239565:2 0:4 170 gold_standard +SRR12204848.15085913 NC_030922.1 NC_030922.1 1239565 1239565 369 NC_030922.1 NC_030922.1 1239565 1239565 369 369 123 12 110 23 1 0 2227 2028 0 0 75S65M 105S6M31S 140 142 CTGGCTACCCTGACTATGATGATGAGGATTACTATGATGAAGATGATGATGGATGGGGAATGGTTGGTGATGATGTAGAATTTGATTATACTGAAGTAATTAATTTTGACCAAACAAAACCAACTCCTGCCCCGAGAACA GCCCAATTGAATTCCGCTGTTGAAAACCCAGTAACTGCCATTACACAACAACCTGTCGTTGCACTAGAACAGAAAAGTGTTAGCGATAGCGATGTGGTTGACCTTGTCAGAACTGCAATGGAACGTGAGATGAAGGTGCTGC FF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFF FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F,FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF:FFFFFFF:FFFFF, 24.890509972401667 2.421392001884805 24.890509972401667 CP True Mamastrovirus 1 1239565 1 283 0:6 1239565:13 39733:3 1239565:8 39733:2 0:74 A:34 1868658:9 39733:5 1868658:1 0:94 NA gold_standard +SRR12204848.28156033 NC_030922.1 NC_030922.1 1239565 1239565 442 NC_030922.1 NC_030922.1 1239565 1239565 442 442 164 234 16 None 15 6 1855 1547 17 17 134M 136M 134 136 CACAACAACCTGTCGTTGCACTAGAACAGAAAAGTGTTAGCGATAGCGATGTGGTTGACCTCGTCAGAACTGCAATGGAACGTGAGATGAAGGTGCTGCGTGATGAAATTAATGGTATACTTGCACCATTCCTA CACAGTAATGGCTTATGTGAATGAAGATCTTGTGGTCTCAACCGCAGCAGCTATTGTACATGGCAACACCCTCTCATATGCAGTTCGCACCCAAGATGGGATGTCGGGTGCACCAGTTTGTGACAAGTATGGTCGA ,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:F:FF,FFFFFFFFFFFFFFF,:FFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFF 33.484149481909085 47.63208599883977 47.63208599883977 CP True Human astrovirus 1868658 1 271 0:11 1868658:5 0:6 1868658:17 0:9 1868658:1 0:51 A:34 0:15 1239565:3 0:1 1239565:5 0:11 1239565:5 0:5 1239565:2 0:54 1239565:2 NA gold_standard +SRR12204848.31434798 NC_001943.1 NC_001943.1 1868658 1868658 235 NC_001943.1 NC_001943.1 1868658 1868658 235 235 216 225 None 18 8 9 1278 1179 18 18 136M 144M3S 136 147 TGTGGCCACTGTACCAACTAGGATAAAAAATGTAGCATTTGACTTCTTTCAGAAGCTGAAACAGTCAGGGGTGCGTGTTGGAGTCAATGAATTTGTTGTCATAAAACCAGGTGCATTATGTGTTATAGACACTCCT CACGTCATTGTTTGTTGTCATACTAACCTGTAGGTTTATACGTATGGCAACAGTTTTTATTGGCACCAGGTTTGAGATCCGTGATGCTAACGGGAAGGTTGTGGCCACTGTACCAACTAGGATAAAAAATGTAGCATTTGACTTCTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF 43.9680793835444 45.08627179858065 45.08627179858065 CP True Human astrovirus 1868658 1 235 1868658:12 0:92 1868658:3 0:16 1239565:2 0:63 1868658:8 0:2 1868658:3 235 gold_standard +SRR12204848.39902754 NC_022249.1 NC_022249.1 1389204 1389204 277 NC_022249.1 NC_022249.1 1389204 1389204 277 277 23 103 18 133 1 23 4486 4337 2 2 30S15M97S 16S52M1D6M2D71M 142 145 TCCATACTTTGGGTAGGACTATGTCATCCTACCAAAACCAGCAATTTACCGGAGGGCTGTTTCTTGTGGAGCTTGCCTCTGAGTGGTGCTTTACAGGCTATGCTGCAAATCCAAACCTTGTTAACTTAATGAAGTCGACCGA ATCTAGGCCTCGATCTCAATCCAGAGGCCGAGACAAATCAGTCAAAATTACAGTTAATTCCAGAAACAAAGGTAGAAGACAAAACGGACGCAACAAACATCAATCTAATCAACGTGTCCGTAACATTGTCAATAAAAAACTCAGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF FFFFFFFFFFFFFFFF,FFFFF::FFFFF:F:F,FFFF,FFFF:FFF:FF,FFFFFFF:FFFF:FFF:F,F,FFFFF,::FF,,FFFF,FFFF::FFFFF:FFF:FFF:,FF,F,FFF::FFF,F,F,FFFFFF:F,FFFFF:F, 4.641001336945877 20.696305113140944 20.696305113140944 CP False unclassified 0 0 288 0:108 A:34 0:112 NA gold_standard +SRR12204848.58209445 NC_030922.1 NC_030922.1 1239565 1239565 458 NC_030922.1 NC_030922.1 1239565 1239565 458 458 165 229 18 159 13 7 2868 2538 17 17 1S128M 138M 129 138 CCCATTATTAGGTCATTTACCAATCAATAGACCCATTTTTGATGATAAGAAACCCAGGGATGATCTCCTTGGTCTACTCCCAGAACCAACCTGGCATGCTTTTGAGGAATATGGACCAACTACATGGGG TTTATCTTGCCAGCGCCACACCGACTAACTAAAGCTGATGAAATAGTTCTTGGATCAAAAATTGTTAAGCTTAGGACGATTATTGAAACAGCCATAAAGACCCAGAACTATAGTGCACTACCTGAAGCTGTGTTTGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFF,F,FFFFFFFFFFFFFFFFFFF:F,FFFFFFFFFF,FF:FFFFFFFFFFFFF,FFFFFFFFFFF 33.951927825838055 46.47619437372113 46.47619437372113 CP True Mamastrovirus 1 1239565 1 268 0:71 1868658:5 0:19 A:34 0:1 1239565:5 0:17 1239565:1 0:35 1239565:5 0:1 1239565:10 0:30 NA gold_standard +SRR12204849.101995294 NC_025675.1 NC_025675.1 1562064 1562064 421 NC_025675.1 NC_025675.1 1562064 1562064 421 421 221 179 None 18 4 13 6033 5737 18 18 125M 135M 125 135 GCTGGAGCACACGGGATAGGCATGGCTGCCATCATCTCGCAAGAGATGCTGGAGGCTGTGTTTACACTCGGTGAGTTCCAAGGTAAAATACACACAGTGAAAGAACACCCCTACATCTATACCCC TGAATTGGGCAAAAACACCAGGTAGACAATTCAGAGAGATCTCTGGATACTTTCCTCGCGGCAAAGAAGGACATTTCAAACTGAGCCCTGCCGCAAAAATTACAGGGGTAGTGGCCCATCAAAATCCCAGCTTTA FA-JJJJJJJJJJJFA