mlst

MLST

About: |

Scan contig files against traditional PubMLST typing schemes

Documentation : https://github.com/tseemann/mlst

Citation : |

The mlst software incorporates components of the PubMLST database which must be cited in any publications that use mlst: "This publication made use of the PubMLST website (https://pubmlst.org/) developed by Keith Jolley (Jolley & Maiden 2010, BMC Bioinformatics, 11:595) and sited at the University of Oxford. The development of that website was funded by the Wellcome Trust".

Directory tree:

mlst
├── mlst_summary.tsv
└── sample_mlst.tsv

Example file for an individual sample (sample_mlst.tsv)

sample	filename	matching PubMLST scheme	ST	ID1	ID2	ID3	ID4	ID5	ID6	ID7	ID8	ID9	ID10	ID11	ID12	ID13	ID14	ID15
Acinetobacter_GCF_008632635.1	Acinetobacter_GCF_008632635.1.fasta	abaumannii_2	46	Pas_cpn60(5)	Pas_fusA(12)	Pas_gltA(11)	Pas_pyrG(2)	Pas_recA(14)	Pas_rplB(9)	Pas_rpoB(14)

Example file for a run (mlst_summary.tsv)

sample	filename	matching PubMLST scheme	ST	ID1	ID2	ID3	ID4	ID5	ID6	ID7	ID8	ID9	ID10	ID11	ID12	ID13	ID14	ID15
Acinetobacter_GCF_008632635.1	Acinetobacter_GCF_008632635.1.fasta	abaumannii_2	46	Pas_cpn60(5)	Pas_fusA(12)	Pas_gltA(11)	Pas_pyrG(2)	Pas_recA(14)	Pas_rplB(9)	Pas_rpoB(14)
burkholderia_GCF_009586235.1	burkholderia_GCF_009586235.1.fasta	bcc	-	atpD(700)	gltB(354)	gyrB(1386?)	recA(769)	lepA(38)	phaC(93)	trpB(828)
cronobacter_GCF_001277215.2	cronobacter_GCF_001277215.2.fasta	cronobacter	7	atpD(10)	fusA(7)	glnS(6)	gltB(7)	gyrB(9)	infB(14)	pps(9)
ecoli_GCA_003019175.1	ecoli_GCA_003019175.1.fasta	ecoli_achtman_4	21	adk(16)	fumC(4)	gyrB(12)	icd(16)	mdh(9)	purA(7)	recA(7)
ecoli_GCA_009738455.1	ecoli_GCA_009738455.1.fasta	ecoli_achtman_4	11	adk(12)	fumC(12)	gyrB(8)	icd(12)	mdh(15)	purA(2)	recA(2)
ecoli_GCA_023823105.1	ecoli_GCA_023823105.1.fasta	ecoli_achtman_4	4040	adk(34)	fumC(36)	gyrB(249)	icd(25)	mdh(28)	purA(16)	recA(4)
kleb_GCF_000240185.1	kleb_GCF_000240185.1.fasta	klebsiella	11	gapA(3)	infB(3)	mdh(1)	pgi(1)	phoE(1)	rpoB(1)	tonB(4)
kleb_GCF_003812925.1	kleb_GCF_003812925.1.fasta	koxytoca	59	gapA(2)	infB(2)	mdh(2)	pgi(27)	phoE(2)	rpoB(1)	tonB(2)
kleb_GCF_015139575.1	kleb_GCF_015139575.1.fasta	koxytoca	-	gapA(12)	infB(29)	mdh(17)	pgi(9)	phoE(20)	rpoB(57)	tonB(~114)
legionella_GCA_001753085.1	legionella_GCA_001753085.1.fasta	-	-
myco_GCF_000195955.2	myco_GCF_000195955.2.fasta	mycobacteria_2	215	S14Z(17)	L35(15)	S19(20)	L19(19)	S12(20)	S8(18)	L16(22)	S7(19)
ralstonia_GCF_021173085.1	ralstonia_GCF_021173085.1.fasta	-	-
salm_GCA_001652385.2	salm_GCA_001652385.2.fasta	senterica_achtman_2	36	aroC(18)	dnaN(14)	hemD(12)	hisD(9)	purE(5)	sucA(18)	thrA(21)
salm_GCA_013344545.1	salm_GCA_013344545.1.fasta	senterica_achtman_2	210	aroC(74)	dnaN(6)	hemD(70)	hisD(8)	purE(7)	sucA(79)	thrA(13)
salm_GCA_019710395.3	salm_GCA_019710395.3.fasta	senterica_achtman_2	34	aroC(10)	dnaN(19)	hemD(12)	hisD(9)	purE(5)	sucA(9)	thrA(2)
shinella_GCF_020883495.1	shinella_GCF_020883495.1.fasta	-	-
strep1_GCA_001412635.1	strep1_GCA_001412635.1.fasta	-	-
strep1_GCA_016724885.1	strep1_GCA_016724885.1.fasta	sdysgalactiae	298	gki(39)	gtr(43)	murI(35)	mutS(33)	recP(47)	xpt(64)	atoB(39)
strep1_GCA_900475035.1	strep1_GCA_900475035.1.fasta	spyogenes	103	gki(2)	gtr(2)	murI(2)	mutS(3)	recP(37)	xpt(3)	yqiL(2)
streppneumo_GCA_000221985.1	streppneumo_GCA_000221985.1.fasta	spneumoniae	-	aroE(427)	gdh(576)	gki(578)	recP(403)	spi(442)	xpt(784)	ddl(656?)
streppneumo_GCA_002076835.1	streppneumo_GCA_002076835.1.fasta	spneumoniae	226	aroE(7)	gdh(13)	gki(42)	recP(6)	spi(10)	xpt(6)	ddl(14)
vibrio_GCA_002953375.1	vibrio_GCA_002953375.1.fasta	vibrio	-	gyrB(~232)	pyrH(~92)	recA(~111)	atpA(~163)
vibrio_GCA_004355205.1	vibrio_GCA_004355205.1.fasta	vvulnificus	446	glp(3)	gyrB(3)	mdh(3)	metG(4)	purM(4)	dtdS(165)	lysA(160)	pntA(1)	pyrC(1)	tnaA(99)
vibrio_GCA_009665315.1	vibrio_GCA_009665315.1.fasta	vibrio	-	gyrB(26)	pyrH(22)	recA(~24)	atpA(20)
vibrio_GCA_009665515.2	vibrio_GCA_009665515.2.fasta	vcholerae	69	adk(7)	gyrB(11)	mdh(4)	metE(37)	pntA(12)	purM(1)	pyrC(20)
vibrio_GCA_009763645.1	vibrio_GCA_009763645.1.fasta	vparahaemolyticus	36	dnaE(21)	gyrB(15)	recA(1)	dtdS(23)	pntA(23)	pyrC(21)	tnaA(16)