quast

Quast

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QUAST evaluates genome assemblies.

Documentation : https://quast.sourceforge.net/quast.html

Citation : https://academic.oup.com/bioinformatics/article/29/8/1072/228832

Directory tree:

quast
├── quast_report.tsv
├── sample
│   ├── basic_stats
│   │   ├── cumulative_plot.pdf
│   │   ├── GC_content_plot.pdf
│   │   ├── Nx_plot.pdf
│   │   └── sample_GC_content_plot.pdf
│   ├── icarus.html
│   ├── icarus_viewers
│   │   └── contig_size_viewer.html
│   ├── quast.log
│   ├── report.html
│   ├── report.pdf
│   ├── report.tex
│   ├── report.tsv
│   ├── report.txt
│   ├── transposed_report.tex
│   ├── transposed_report.tsv
│   └── transposed_report.txt
└── sample_quast_report.tsv

Example file for an individual sample (sample/report.tsv)

Assembly	Acinetobacter_GCF_008632635.1
# contigs (>= 0 bp)	2
# contigs (>= 1000 bp)	2
# contigs (>= 5000 bp)	2
# contigs (>= 10000 bp)	1
# contigs (>= 25000 bp)	1
# contigs (>= 50000 bp)	1
Total length (>= 0 bp)	3980230
Total length (>= 1000 bp)	3980230
Total length (>= 5000 bp)	3980230
Total length (>= 10000 bp)	3972439
Total length (>= 25000 bp)	3972439
Total length (>= 50000 bp)	3972439
# contigs	2
Largest contig	3972439
Total length	3980230
GC (%)	38.99
N50	3972439
N90	3972439
auN	3964678.5
L50	1
L90	1
# N's per 100 kbp	0.00

Example file for a run (quast_report.tsv)

sample	Assembly	# contigs (>= 0 bp)	# contigs (>= 1000 bp)	# contigs (>= 5000 bp)	# contigs (>= 10000 bp)	# contigs (>= 25000 bp)	# contigs (>= 50000 bp)	Total length (>= 0 bp)	Total length (>= 1000 bp)	Total length (>= 5000 bp)	Total length (>= 10000 bp)	Total length (>= 25000 bp)	Total length (>= 50000 bp)	# contigs	Largest contig	Total length	GC (%)	N50	N90	auN	L50	L90	# N's per 100 kbp
Acinetobacter_GCF_008632635.1	Acinetobacter_GCF_008632635.1	2	2	2	1	1	1	3980230	3980230	3980230	3972439	3972439	3972439	2	3972439	3980230	38.99	3972439	3972439	3964678.5	1	1	0.00
burkholderia_GCF_009586235.1	burkholderia_GCF_009586235.1	3	3	3	3	3	3	8366868	8366868	8366868	8366868	8366868	8366868	3	3688624	8366868	66.75	3430130	1248114	3218591.2	2	3	0.00
cronobacter_GCF_001277215.2	cronobacter_GCF_001277215.2	3	3	3	3	3	3	4473761	4473761	4473761	4473761	4473761	4473761	3	4294639	4473761	56.85	4294639	4294639	4126884.6	1	1	0.00
ecoli_GCA_003019175.1	ecoli_GCA_003019175.1	2	2	2	2	2	2	5605298	5605298	5605298	5605298	5605298	5605298	2	5509931	5605298	50.65	5509931	5509931	5417809.1	1	1	0.00
ecoli_GCA_009738455.1	ecoli_GCA_009738455.1	2	2	2	2	2	2	5609319	5609319	5609319	5609319	5609319	5609319	2	5511015	5609319	50.43	5511015	5511015	5416156.6	1	1	0.00
ecoli_GCA_023823105.1	ecoli_GCA_023823105.1	5	5	5	5	5	5	5044697	5044697	5044697	5044697	5044697	5044697	5	4743616	5044697	50.59	4743616	4743616	4465289.2	1	1	0.00
kleb_GCF_000240185.1	kleb_GCF_000240185.1	7	7	4	4	4	4	5682322	5682322	5673910	5673910	5673910	5673910	7	5333942	5682322	57.12	5333942	5333942	5013731.8	1	1	0.02
kleb_GCF_003812925.1	kleb_GCF_003812925.1	3	3	3	1	1	1	5879076	5879076	5879076	5864574	5864574	5864574	3	5864574	5879076	55.13	5864574	5864574	5850126.1	1	1	0.00
kleb_GCF_015139575.1	kleb_GCF_015139575.1	2	2	2	2	2	2	6041841	6041841	6041841	6041841	6041841	6041841	2	5935402	6041841	55.99	5935402	5935402	5832713.3	1	1	0.00
legionella_GCA_001753085.1	legionella_GCA_001753085.1	3	3	3	3	3	2	3504074	3504074	3504074	3504074	3504074	3470715	3	3397139	3504074	38.33	3397139	3397139	3295329.8	1	1	0.00
myco_GCF_000195955.2	myco_GCF_000195955.2	1	1	1	1	1	1	4411532	4411532	4411532	4411532	4411532	4411532	1	4411532	4411532	65.61	4411532	4411532	4411532.0	1	1	0.00
ralstonia_GCF_021173085.1	ralstonia_GCF_021173085.1	2	2	2	2	2	2	5310536	5310536	5310536	5310536	5310536	5310536	2	3505964	5310536	63.74	3505964	1804572	2927814.4	1	2	0.00
salm_GCA_001652385.2	salm_GCA_001652385.2	2	2	2	2	2	2	4930422	4930422	4930422	4930422	4930422	4930422	2	4855022	4930422	52.11	4855022	4855022	4781928.2	1	1	0.00
salm_GCA_013344545.1	salm_GCA_013344545.1	3	3	3	2	2	2	5038048	5038048	5038048	5031811	5031811	5031811	3	4781872	5038048	51.87	4781872	4781872	4551129.4	1	1	0.00
salm_GCA_019710395.3	salm_GCA_019710395.3	2	2	2	2	2	2	5019039	5019039	5019039	5019039	5019039	5019039	2	4934155	5019039	52.19	4934155	4934155	4852142.2	1	1	0.00
shinella_GCF_020883495.1	shinella_GCF_020883495.1	5	5	5	5	5	4	4848065	4848065	4848065	4848065	4848065	4813360	5	3991891	4848065	64.43	3991891	372552	3342126.1	1	2	0.00
strep1_GCA_001412635.1	strep1_GCA_001412635.1	1	1	1	1	1	1	1924513	1924513	1924513	1924513	1924513	1924513	1	1924513	1924513	38.99	1924513	1924513	1924513.0	1	1	0.00
strep1_GCA_016724885.1	strep1_GCA_016724885.1	3	3	2	1	1	1	2151179	2151179	2147828	2141294	2141294	2141294	3	2141294	2151179	39.34	2141294	2141294	2131479.5	1	1	0.00
strep1_GCA_900475035.1	strep1_GCA_900475035.1	1	1	1	1	1	1	1746380	1746380	1746380	1746380	1746380	1746380	1	1746380	1746380	38.55	1746380	1746380	1746380.0	1	1	0.00
streppneumo_GCA_000221985.1	streppneumo_GCA_000221985.1	2	2	1	1	1	1	2195458	2195458	2190731	2190731	2190731	2190731	2	2190731	2195458	39.79	2190731	2190731	2186024.4	1	1	0.00
streppneumo_GCA_002076835.1	streppneumo_GCA_002076835.1	2	2	2	1	1	1	2154362	2154362	2154362	2148350	2148350	2148350	2	2148350	2154362	39.54	2148350	2148350	2142371.6	1	1	1721.86
vibrio_GCA_002953375.1	vibrio_GCA_002953375.1	2	2	2	2	2	2	4867548	4867548	4867548	4867548	4867548	4867548	2	3150565	4867548	50.18	3150565	1716983	2644882.1	1	2	0.00
vibrio_GCA_004355205.1	vibrio_GCA_004355205.1	2	2	2	2	2	2	5199428	5199428	5199428	5199428	5199428	5199428	2	3336880	5199428	46.75	3336880	1862548	2808742.3	1	2	3.85
vibrio_GCA_009665315.1	vibrio_GCA_009665315.1	2	2	2	2	2	2	5751647	5751647	5751647	5751647	5751647	5751647	2	3531034	5751647	44.96	3531034	2220613	3025102.8	1	2	0.00
vibrio_GCA_009665515.2	vibrio_GCA_009665515.2	2	2	2	2	2	2	4098803	4098803	4098803	4098803	4098803	4098803	2	3051680	4098803	47.50	3051680	1047123	2539574.9	1	2	2.44
vibrio_GCA_009763645.1	vibrio_GCA_009763645.1	2	2	2	2	2	2	5197133	5197133	5197133	5197133	5197133	5197133	2	3343366	5197133	45.31	3343366	1853767	2812040.5	1	2	0.00