serotypefinder

SerotypeFinder

About: |

SerotypeFinder identifies the serotype in total or partial sequenced isolates of E. coli.

Documentation : https://bitbucket.org/genomicepidemiology/serotypefinder/overview

Citation :

Directory tree:

serotypefinder/
├── sample
│   ├── data.json
│   ├── Hit_in_genome_seq.fsa
│   ├── results_tab.tsv
│   ├── results.txt
│   ├── Serotype_allele_seq.fsa
│   └── tmp
│       ├── out_H_type.xml
│       └── out_O_type.xml
├── sample_serotypefinder.tsv
└── serotypefinder_results.txt

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

Database	Gene	Serotype	Identity	Template / HSP length	Contig	Position in contig	Accession number
H_type	fliC	H11	99.93	1459 / 1467	CP027546.1 Escherichia coli strain 2013C-4187 chromosome, complete genome	1705597..1707055	AY337465
O_type	wzy	O71	100.0	1290 / 1290	CP027546.1 Escherichia coli strain 2013C-4187 chromosome, complete genome	1839531..1840820	GU445927
O_type	wzx	O71	100.0	1275 / 1275	CP027546.1 Escherichia coli strain 2013C-4187 chromosome, complete genome	1842225..1843499	GU445927

Example file for a run (serotypefinder_results.txt)

sample	Database	Gene	Serotype	Identity	Template / HSP length	Contig	Position in contig	Accession number
ecoli_GCA_003019175.1	H_type	fliC	H11	99.93	1459 / 1467	CP027546.1 Escherichia coli strain 2013C-4187 chromosome, complete genome	1705597..1707055	AY337465
ecoli_GCA_003019175.1	O_type	wzy	O71	100.0	1290 / 1290	CP027546.1 Escherichia coli strain 2013C-4187 chromosome, complete genome	1839531..1840820	GU445927
ecoli_GCA_003019175.1	O_type	wzx	O71	100.0	1275 / 1275	CP027546.1 Escherichia coli strain 2013C-4187 chromosome, complete genome	1842225..1843499	GU445927
ecoli_GCA_009738455.1	H_type	fliC	H7	100.0	1758 / 1758	CP046527.1 Escherichia coli strain RM19259 chromosome, complete genome	5128276..5130033	AF228487
ecoli_GCA_009738455.1	O_type	wzx	O157	100.0	1287 / 1287	CP046527.1 Escherichia coli strain RM19259 chromosome, complete genome	5344341..5345627	AKMA01000036
ecoli_GCA_009738455.1	O_type	wzy	O157	100.0	1185 / 1185	CP046527.1 Escherichia coli strain RM19259 chromosome, complete genome	5346434..5347618	JH953200
ecoli_GCA_009738455.1	O_type	wzx	O157	100.0	1392 / 1392	CP046527.1 Escherichia coli strain RM19259 chromosome, complete genome	5344341..5345732	JH959508
ecoli_GCA_023823105.1	H_type	fliC	H15	100.0	1689 / 1689	CP090402.1 Shigella sp. PIB chromosome, complete genome	1961225..1962913	AY249999
ecoli_GCA_023823105.1	O_type	wzx	O1	100.0	1227 / 1227	CP090402.1 Shigella sp. PIB chromosome, complete genome	1868664..1869890	GU299791
ecoli_GCA_023823105.1	O_type	wzy	O1	99.7	1005 / 1005	CP090402.1 Shigella sp. PIB chromosome, complete genome	1872158..1873162	GU299791