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Overview of the filtering process within the amr.watch workflow applied to public genomes of priority bacterial pathogens available in the International Nucleotide Sequence Database Collaboration (INSDC) databases. The genome data are filtered in a series of steps, depicted from left to right in the table, with the numbers in each column representing a subset of those from the previous column.

For the pathogens that are grouped together, we initially accept genomes annotated in the ENA with any of the corresponding taxonomy IDs from the same group and use the Speciator assignments in subsequent processing.

PathogenENA entries (run accessions)Illumina paired-end entriesFiltered entries1Entries with geotemporal data2Entries available for download in SRAEntries associated with unique samples3Assembled genomesGenomes with correct speciesGenomes that passed QCGenomes with collection date post-2010Last updated
All Pathogens 1,781,1771,572,6411,525,910900,390885,192851,696823,550803,248782,011717,252
A. baumannii 52,33442,66039,68527,20426,69125,87025,52325,15724,72923,193
C. coli 178,158173,157167,531113,958112,598111,989109,72933,82332,55131,420
C. jejuni 74,10970,79968,287
E. cloacae complex 22,66119,93119,16614,64414,51313,26212,90112,47811,84611,386
E. faecium 45,83143,76642,52226,90526,60325,52925,34225,08924,74723,498
E. coli 649,082541,157530,075305,903300,882289,708281,137242,040237,931218,323
S. flexneri 14,17213,74612,965
S. sonnei 16,39015,92814,948
H. influenzae 18,94117,37717,2688,4118,3868,0877,4557,4387,2746,658
K. pneumoniae 136,562119,375110,04171,37269,78964,22962,38060,12458,38856,317
N. gonorrhoeae 84,04479,93179,42753,62753,13049,82646,70346,29644,21743,433
P. aeruginosa 87,57863,57460,51232,35531,71330,57628,72528,36127,43625,720
Salmonella Typhi 131,495122,420120,91094,25294,02992,00490,6859,1478,9756,937
Salmonella Typhimurium 28,38527,65525,479
Salmonella Enteritidis 49,05648,17746,495
S. aureus 186,492169,037162,26494,09689,62185,74381,79880,36577,93266,177
S. pneumoniae 187,999180,256176,50957,66357,23754,87351,17250,81849,68036,016

  1. Entries (runs) are filtered to include only those with two FASTQ files, ≥20x mean coverage (via assessment of the "base_count" field) and those associated with a single sample accession.
  2. Entries (runs) are filtered to include those with a collection date that is decodable to at least the year and a sampling location that is decodable to at least the country level.
  3. Entries (runs) are filtered to ensure only one run per sample accession is included (selecting the run with the highest number of bases via assessment of the "base_count" field).