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Jody E. Phelan et al.
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J. W. A. Rossen et al.
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Marc W. Allard et al.
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Quang Huy Nguyen et al.
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Philip T. L. C. Clausen et al.
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Matthew Ezewudo et al.
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Thomas Andreas Kohl et al.
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A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis
Paolo Miotto et al.
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Ea Zankari et al.
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Varvara K. Kozyreva et al.
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Viola Schleusener et al.
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Leihong Wu et al.
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J. Ronholm et al.
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Merly Escalona et al.
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Silke Feuerriegel et al.
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Phelim Bradley et al.
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Best practices for evaluating single nucleotide variant calling methods for microbial genomics
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KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes
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Prapaporn Srilohasin et al.
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Francesc Coll et al.
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SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Michael Inouye et al.
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Andreas Roetzer et al.
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SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences
Francesc Coll et al.
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Snakemake-a scalable bioinformatics workflow engine
Johannes Koester et al.
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Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
Mette V. Larsen et al.
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Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
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Heng Li
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Web-Accessible Database of hsp65 Sequences from Mycobacterium Reference Strains
Jianli Dai et al.
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The Sequence Read Archive
Rasko Leinonen et al.
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BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
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BIGSdb: Scalable analysis of bacterial genome variation at the population level
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Heng Li et al.
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Circos: An information aesthetic for comparative genomics
Martin Krzywinski et al.
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Karine Brudey et al.
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CS Bakshi et al.
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H Kim et al.
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L Herrera-Leon et al.
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