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Table 2 Testing the pipeline on artificial WGS data

From: BacTag - a pipeline for fast and accurate gene and allele typing in bacterial sequencing data based on database preprocessing

Species and strain

GeneBank Accession number

Identified alleles

E. coli 042

FN554766.1

adk-18, fumC-22, gyrB-20, Icd-23, mdh-5, purA-15, recA-4

E. coli E2348/69

FM180568.1

adk-15, fumC-15, gyrB-11, Icd-15, mdh-18, purA-11, recA-11

E. coli E24377A

CP000800.1

adk-6, fumC-213, gyrB-33, Icd-1, mdh-24, purA-8, recA-7

E. coli IHE3034

NC_017628.1

adk-37, fumC-38, gyrB-19, Icd-37, mdh-17, purA-11, recA-26

E. coli IMT5155

CP005930.1

adk-55, fumC-38, gyrB-19, Icd-37, mdh-17, purA-11, recA-26

E. coli RS218

NZ_CP007149.1

adk-37, fumC-38, gyrB-19, Icd-37, mdh-17, purA-11, recA-26

E. coli UMN026

NC_011751.1

adk-21, fumC-35, gyrB-115, Icd-6, mdh-5, purA-5, recA-4

S. pseudintermedius NA45

NZ_CP016072.1

ack-2, cpn60–10, fdh-2, pta-1, purA-5, sar-1, tuf-2

S. pseudintermedius ED99

NC_017568.1

ack-3, cpn60–9, fdh-2, pta-1, purA-1, sar-1, tuf-1

S. pseudintermedius HKU10–03

NC_014925.1

ack-2, cpn60–55, fdh-3, pta-42, purA-14, sar-2, tuf-1

M. bovis Ningxia-1

NZ_CP023663.1

adh1–4, gltX-3, gpsA-2, gyr-3, pta2–17, tdk-3, tkt-4

M. bovis HB0801

NC_018077.1

adh1–4, gltX-3, gpsA-2, gyr-3, pta2–5, tdk-3, tkt-4

M. bovis NM2012

NZ_CP011348.1

adh1–4, gltX-3, gpsA-2, gyr-3, pta2–5, tdk-3, tkt-4

M. bovis CQ-W70

NC_015725.1

adh1–4, gltX-5, gpsA-2, gyr-3, pta2–5, tdk-3, tkt-4

M. bovis PG45

NC_014760.1

adh1–3, gltX-2, gpsA-4, gyr-2, pta2–1, tdk-3, tkt-2

M. bovis 08 M

NZ_CP019639.1

adh1–4, gltX-3, gpsA-2, gyr-3, pta2–5, tdk-3, tkt-4

P. gingivalis ATCC 33277

NC_010729.1

ftsQ-5, gpdxJ-9, hagB-1, mcmA-1, pepO-1, pga-5, recA-5

P. gingivalis AJW4

NZ_CP011996.1

ftsQ-21, gpdxJ-23, hagB-1, mcmA-3, pepO-20, pga-3, recA-7

P. gingivalis A7A1–28

CP013131.1

ftsQ-1, gpdxJ-12, hagB-1, mcmA-1, pepO-1, pga-1, recA-1

Borrelia hermsii DAH

NC_010673.1

clpA-68, clpX-165, nifS-149, pepX-171, pyrG-179, recG-188, rplB-157, uvrA-175

Borrelia turicatae 91E135

NC_008710.1

clpA-71, clpX-166, nifS-150, pepX-172, pyrG-180, recG-189, rplB-158, uvrA-176

Borrelia anserina BA2

CP005829

clpA-212, clpX-179, nifS-161, pepX-186, pyrG-196, recG-204, rplB-170, uvrA-188

Borrelia recurrentis A1

NC_011244

clpA-213, clpX-164, nifS-162, pepX-187, pyrG-197, recG-205, rplB-156, uvrA-189

Borrelia parkeri SLO

CP005851

clpA-214, clpX-180, nifS-163, pepX-188, pyrG-198, recG-206, rplB-171, uvrA-190

Borrelia coriaceae Co53

CP005745

clpA-215, clpX-181, nifS-164, pepX-189, pyrG-199, recG-207, rplB-172, uvrA-191

Borrelia crocidurae Achema

CP003426

clpA-216, clpX-164, nifS-165, pepX-190, pyrG-200, recG-208, rplB-173, uvrA-192

Streptomyces coelicolor A3(2)

NC_003888.3

atpD-127, gyrB-124, recA-131, rpoB-126, trpB-142

Streptomyces fulvissimus DSM 40593

CP005080.1

atpD-133, gyrB-130, recA-13, rpoB-36, trpB-147

Streptomyces griseus NBRC 13350

NC_010572.1

atpD-6, gyrB-8, recA-8, rpoB-8, trpB-8

Streptomyces albidoflavus J1074

NC_020990.1

atpD-36, gyrB-5, recA-5, rpoB-36, trpB-39