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Young edited this page Apr 22, 2024 · 2 revisions

kaptive

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Kaptive is a system for surface polysaccharide typing from bacterial genome sequences. It consists of two main components:

Documentation : https://kaptive.readthedocs.io/en/latest/

Citation : https://doi.org/10.1099/mgen.0.000102

Directory tree:

kaptive/
├── kaptive_summary.txt
├── sample_table.txt
├── sample_ref.json
├── sample_ref_contigs.fasta
└── sample_ref_table.txt

Example file for an individual sample (SRR15050763_VibrioPara_Kaptivedb_K_table.txt)

Assembly        Best match locus        Best match type Match confidence        Problems        Coverage        Identity        Length discrepancy      Expected genes in locus Expected genes in locus, details        Missing expected genes  Other genes in locus    Other genes in locus, details   Expected genes outside locus    Expected genes outside locus, details     Other genes outside locus       Other genes outside locus, details
SRR15050763_contigs     KL38            None    ?-+*    45.12%  69.72%  n/a     1 / 19 (5.3%)   KL38_17_wvcI,86.74%     KL38_01;KL38_02;KL38_03_gfcB;KL38_04;KL38_05;KL38_06_kpsD;KL38_07_wzzE;KL38_08;KL38_09;KL38_10;KL38_11;KL38_12;KL38_13;KL38_14;KL38_15_pglA;KL38_16_rmlB;KL38_18_wvcK;KL38_19_ugd       2       KLUT7_23_ugd,80.72%;KL54_08,81.102%       0 / 19 (0%)             4       KL50_19_manC1,80.932%;KL147_31_rmlA_2,86.458%;KL28_10_cysD,80.667%;KL137_17_kdsA,86.972%

Example file for a run (kaptive_summary.txt)

Assembly        Best match locus        Best match type Match confidence        Problems        Coverage        Identity        Length discrepancy      Expected genes in locus Expected genes in locus, details        Missing expected genes  Other genes in locus    Other genes in locus, details   Expected genes outside locus    Expected genes outside locus, details     Other genes outside locus       Other genes outside locus, details
SRR15050763_contigs     KL38            None    ?-+*    45.12%  69.72%  n/a     1 / 19 (5.3%)   KL38_17_wvcI,86.74%     KL38_01;KL38_02;KL38_03_gfcB;KL38_04;KL38_05;KL38_06_kpsD;KL38_07_wzzE;KL38_08;KL38_09;KL38_10;KL38_11;KL38_12;KL38_13;KL38_14;KL38_15_pglA;KL38_16_rmlB;KL38_18_wvcK;KL38_19_ugd       2       KLUT7_23_ugd,80.72%;KL54_08,81.102%       0 / 19 (0%)             4       KL50_19_manC1,80.932%;KL147_31_rmlA_2,86.458%;KL28_10_cysD,80.667%;KL137_17_kdsA,86.972%
SRR15050763_contigs     OL101           None    ?-      38.15%  71.60%  n/a     0 / 8 (0%)              OL101_01_kdkA;OL101_02_wvaK;OL101_03_wvaL;OL101_04_wvaQ;OL101_05_wvaR;OL101_06_kdtA;OL101_07_waaF;OL101_08_msbB 0               0 / 8 (0%)              0
SRR15200146_contigs     KL65            None    ?-*     50.53%  70.68%  n/a     6 / 20 (30%)    KL65_08_wvaM,87.406%;KL65_09_wvaN,82.292%;KL65_11_wvaO,82.778%;KL65_14_wbpI,88.462%;KL65_17_wvcI,84.53%;KL65_20_rmlA,86.458%    KL65_01;KL65_02;KL65_03_gfcB;KL65_04;KL65_05;KL65_06_kpsD;KL65_07_wzc;KL65_10_gne;KL65_12_wvaP;KL65_13_hddC;KL65_15;KL65_16_rmlB;KL65_18_wvcK;KL65_19_ugd 0               0 / 20 (0%)             6       KL112_12_wvcK_1,90.751%;KL157_16_gmhD_2,81.471%;KL137_17_kdsA,87.324%;KL28_10_cysD,80.0%;KL137_10_kpsT,83.486%;KL54_08,81.102%
SRR15200146_contigs     OL13_or_OL13            None    ?-+*    46.56%  70.45%  n/a     3 / 18 (16.7%)  OL13_or_OL13_02_wvaM,88.917%;OL13_or_OL13_03_wvaN,80.208%;OL13_or_OL13_05_wvaO,82.402%  OL13_or_OL13_01_kdkA;OL13_or_OL13_04_gne;OL13_or_OL13_06_wvaP;OL13_or_OL13_07_hddC;OL13_or_OL13_08_wvaQ;OL13_or_OL13_09_iolG;OL13_or_OL13_10_kat;OL13_or_OL13_11_yafV;OL13_or_OL13_12_wvdC;OL13_or_OL13_13_wvcC;OL13_or_OL13_14_wvaR;OL13_or_OL13_15_wvaH;OL13_or_OL13_16_kdtA;OL13_or_OL13_17_waaF;OL13_or_OL13_18_msbB  1       OL5_12_hddC,81.25%      0 / 18 (0%)             0
SRR15223896_contigs     KL12            Very high               100.00% 99.71%  -22 bp  32 / 32 (100%)  KL12_01,99.864%;KL12_02,100.0%;KL12_03_gfcB,100.0%;KL12_04,100.0%;KL12_05,100.0%;KL12_06,100.0%;KL12_07_kpsD,100.0%;KL12_08_wzzE,100.0%;KL12_09,100.0%;KL12_10,100.0%;KL12_11,100.0%;KL12_12,100.0%;KL12_13,100.0%;KL12_14,100.0%;KL12_15,100.0%;KL12_16,100.0%;KL12_17_wbnK,99.653%;KL12_18,99.738%;KL12_19_ykvP,99.712%;KL12_20_wvaG,99.717%;KL12_21_rmlB_1,100.0%;KL12_22_rmlB_2,100.0%;KL12_23_gmm,100.0%;KL12_24_rmlA,100.0%;KL12_25_glmM,100.0%;KL12_26_manA,100.0%;KL12_27,100.0%;KL12_28_gnu,99.668%;KL12_29_wvcI,100.0%;KL12_30_wvcK,100.0%;KL12_31_ugd,100.0%;KL12_32_rmlB_3,100.0%             00 / 32 (0%)              8       KL156_12_wvaD,98.098%;KL156_08_rmlB,98.873%;KL156_09_rmlA,100.0%;KL103_23_rmlA,87.5%;KL137_17_kdsA,88.732%;KL28_10_cysD,81.333%;KL156_11_wvdI,98.726%;KL156_10_wbtA,99.225%
SRR15223896_contigs     OL4             Very high               100.00% 100.00% 0 bp    19 / 19 (100%)  OL4_01_kdkA,100.0%;OL4_02_rmlB,100.0%;OL4_03_rmlA,100.0%;OL4_04_wbtA,100.0%;OL4_05_wvdI,100.0%;OL4_06_wvaD,100.0%;OL4_07_wvcN,100.0%;OL4_08,100.0%;OL4_09,100.0%;OL4_10,100.0%;OL4_11,100.0%;OL4_12_dprE1,100.0%;OL4_13_wvdC,100.0%;OL4_14,100.0%;OL4_15_kdtA,100.0%;OL4_16_wbnK,100.0%;OL4_17_waaF,100.0%;OL4_18_wvaH,100.0%;OL4_19_msbB,100.0%          0               0 / 19 (0%)             0
SRR15223903_contigs     KL12            Very high               100.00% 99.71%  -22 bp  32 / 32 (100%)  KL12_01,99.864%;KL12_02,100.0%;KL12_03_gfcB,100.0%;KL12_04,100.0%;KL12_05,100.0%;KL12_06,100.0%;KL12_07_kpsD,100.0%;KL12_08_wzzE,100.0%;KL12_09,100.0%;KL12_10,100.0%;KL12_11,100.0%;KL12_12,100.0%;KL12_13,100.0%;KL12_14,100.0%;KL12_15,100.0%;KL12_16,100.0%;KL12_17_wbnK,99.653%;KL12_18,99.738%;KL12_19_ykvP,99.712%;KL12_20_wvaG,99.717%;KL12_21_rmlB_1,100.0%;KL12_22_rmlB_2,100.0%;KL12_23_gmm,100.0%;KL12_24_rmlA,100.0%;KL12_25_glmM,100.0%;KL12_26_manA,100.0%;KL12_27,100.0%;KL12_28_gnu,99.668%;KL12_29_wvcI,100.0%;KL12_30_wvcK,100.0%;KL12_31_ugd,100.0%;KL12_32_rmlB_3,100.0%             00 / 32 (0%)              8       KL156_12_wvaD,98.098%;KL156_08_rmlB,98.873%;KL156_09_rmlA,100.0%;KL103_23_rmlA,87.5%;KL137_17_kdsA,88.732%;KL28_10_cysD,81.333%;KL156_11_wvdI,98.726%;KL156_10_wbtA,99.225%
SRR15223903_contigs     OL4             Very high               100.00% 100.00% 0 bp    19 / 19 (100%)  OL4_01_kdkA,100.0%;OL4_02_rmlB,100.0%;OL4_03_rmlA,100.0%;OL4_04_wbtA,100.0%;OL4_05_wvdI,100.0%;OL4_06_wvaD,100.0%;OL4_07_wvcN,100.0%;OL4_08,100.0%;OL4_09,100.0%;OL4_10,100.0%;OL4_11,100.0%;OL4_12_dprE1,100.0%;OL4_13_wvdC,100.0%;OL4_14,100.0%;OL4_15_kdtA,100.0%;OL4_16_wbnK,100.0%;OL4_17_waaF,100.0%;OL4_18_wvaH,100.0%;OL4_19_msbB,100.0%          0               0 / 19 (0%)             0
SRR16267445_contigs     KL12            Very high               100.00% 99.71%  -22 bp  32 / 32 (100%)  KL12_01,99.864%;KL12_02,100.0%;KL12_03_gfcB,100.0%;KL12_04,100.0%;KL12_05,100.0%;KL12_06,100.0%;KL12_07_kpsD,100.0%;KL12_08_wzzE,100.0%;KL12_09,100.0%;KL12_10,100.0%;KL12_11,100.0%;KL12_12,100.0%;KL12_13,100.0%;KL12_14,100.0%;KL12_15,100.0%;KL12_16,100.0%;KL12_17_wbnK,99.653%;KL12_18,99.738%;KL12_19_ykvP,99.712%;KL12_20_wvaG,99.717%;KL12_21_rmlB_1,100.0%;KL12_22_rmlB_2,100.0%;KL12_23_gmm,100.0%;KL12_24_rmlA,100.0%;KL12_25_glmM,100.0%;KL12_26_manA,100.0%;KL12_27,100.0%;KL12_28_gnu,99.668%;KL12_29_wvcI,100.0%;KL12_30_wvcK,100.0%;KL12_31_ugd,100.0%;KL12_32_rmlB_3,100.0%             00 / 32 (0%)              8       KL156_12_wvaD,98.098%;KL156_08_rmlB,98.873%;KL156_09_rmlA,100.0%;KL103_23_rmlA,87.5%;KL137_17_kdsA,88.732%;KL28_10_cysD,81.333%;KL156_11_wvdI,98.726%;KL156_10_wbtA,99.225%
SRR16267445_contigs     OL4             Very high               100.00% 100.00% 0 bp    19 / 19 (100%)  OL4_01_kdkA,100.0%;OL4_02_rmlB,100.0%;OL4_03_rmlA,100.0%;OL4_04_wbtA,100.0%;OL4_05_wvdI,100.0%;OL4_06_wvaD,100.0%;OL4_07_wvcN,100.0%;OL4_08,100.0%;OL4_09,100.0%;OL4_10,100.0%;OL4_11,100.0%;OL4_12_dprE1,100.0%;OL4_13_wvdC,100.0%;OL4_14,100.0%;OL4_15_kdtA,100.0%;OL4_16_wbnK,100.0%;OL4_17_waaF,100.0%;OL4_18_wvaH,100.0%;OL4_19_msbB,100.0%          0               0 / 19 (0%)             0
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