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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