@@ -103,139 +131,151 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -263,7 +303,7 @@ - use_pointfinder != "disabled" + pointfinder_db['use_pointfinder'] != "disabled" @@ -273,7 +313,7 @@ - + @@ -282,58 +322,69 @@ - - + + - + + + + + + + + + + + + - + - +

- +

- + - + - + - + - + - + @@ -557,17 +608,22 @@ .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db -.. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/ +.. _webservice: https://cge.food.dtu.dk/services/ResFinder/ ]]> - @misc{githubstaramr, - author = {Petkau, Aaron}, - year = {2018}, - title = {staramr}, - publisher = {GitHub}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/staramr}, - } + @Article{microorganisms10020292, + AUTHOR = {Bharat, Amrita and Petkau, Aaron and Avery, Brent P. and Chen, Jessica C. and Folster, Jason P. and Carson, Carolee A. and Kearney, Ashley and Nadon, Celine and Mabon, Philip and Thiessen, Jeffrey and Alexander, David C. and Allen, Vanessa and El Bailey, Sameh and Bekal, Sadjia and German, Greg J. and Haldane, David and Hoang, Linda and Chui, Linda and Minion, Jessica and Zahariadis, George and Domselaar, Gary Van and Reid-Smith, Richard J. and Mulvey, Michael R.}, + TITLE = {Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr}, + JOURNAL = {Microorganisms}, + VOLUME = {10}, + YEAR = {2022}, + NUMBER = {2}, + ARTICLE-NUMBER = {292}, + URL = {https://www.mdpi.com/2076-2607/10/2/292}, + ISSN = {2076-2607}, + DOI = {10.3390/microorganisms10020292} + } + diff -r 4b9a8031ab74 -r be818ae858e4 test-data/mlst.tsv --- a/test-data/mlst.tsv Fri Mar 05 16:04:58 2021 +0000 +++ b/test-data/mlst.tsv Wed Jun 22 14:44:55 2022 +0000 @@ -1,2 +1,2 @@ Isolate ID Scheme Sequence Type Locus 1 Locus 2 Locus 3 Locus 4 Locus 5 Locus 6 Locus 7 -16S-rc_gyrA-rc_beta-lactam.fsa kpneumoniae - gapA(-) infB(-) mdh(-) pgi(-) phoE(-) rpoB(-) tonB(-) +16S-rc_gyrA-rc_beta-lactam.fsa listeria_2 - abcZ(-) bglA(-) cat(-) dapE(-) dat(-) ldh(-) lhkA(-) diff -r 4b9a8031ab74 -r be818ae858e4 test-data/test1-detailed-summary-ecoli.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1-detailed-summary-ecoli.tsv Wed Jun 22 14:44:55 2022 +0000 @@ -0,0 +1,4 @@ +Isolate ID Data Data Type Predicted Phenotype %Identity %Overlap HSP Length/Total Length Contig Start End Accession +16S-rc_gyrA-rc_beta-lactam.fsa ST- (-) MLST +16S-rc_gyrA-rc_beta-lactam.fsa None Plasmid +16S-rc_gyrA-rc_beta-lactam.fsa blaIMP-42 Resistance ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem 99.73 100.0 741/741 16S_rrsD 4381 5121 AB753456 diff -r 4b9a8031ab74 -r be818ae858e4 test-data/test1-pointfinder-ecoli.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1-pointfinder-ecoli.tsv Wed Jun 22 14:44:55 2022 +0000 @@ -0,0 +1,1 @@ +Isolate ID Gene Predicted Phenotype Type Position Mutation %Identity %Overlap HSP Length/Total Length Contig Start End diff -r 4b9a8031ab74 -r be818ae858e4 test-data/test1-summary-ecoli.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1-summary-ecoli.tsv Wed Jun 22 14:44:55 2022 +0000 @@ -0,0 +1,2 @@ +Isolate ID Quality Module Genotype Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback +16S-rc_gyrA-rc_beta-lactam.fsa Failed blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem None - - 5220 5220 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000] diff -r 4b9a8031ab74 -r be818ae858e4 test-data/test6-summary.tsv --- a/test-data/test6-summary.tsv Fri Mar 05 16:04:58 2021 +0000 +++ b/test-data/test6-summary.tsv Wed Jun 22 14:44:55 2022 +0000 @@ -1,2 +1,2 @@ Isolate ID Quality Module Genotype Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback -test-aminoglycoside.fsa Failed aac(6')-Iaa gentamicin None - - 438 438 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000] +test-aminoglycoside.fsa Failed aac(6')-Iaa unknown[aac(6')-Iaa_1_NC_003197] None - - 438 438 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]