SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
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Cites methods from "SRST2: Rapid genomic surveillance f..."
...Inouye M, et al. (2014) SRST2: Rapid genomic surveillance for public health and hospital microbiology labs....
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...STs were assigned to each genome according to the K. pneumoniae MLST database (13) by mapping to known alleles using SRST2 (68)....
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...pneumoniae MLST database (13) by mapping to known alleles using SRST2 (68)....
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...Read sets also were screened for known alleles of important genes using a readmapping approach with SRST2 (68)....
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"SRST2: Rapid genomic surveillance f..." refers methods in this paper
...18 [30] mpileup and parsed by SRST2 to determine percent coverage, divergence, and mismatches as well as to calculate a score for each possible allele....
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Additional excerpts
...There are several assemblers (for example, Velvet [24], SPAdes [25]) that can produce a bacterial genome assembly in minutes to hours with a few gigabytes of memory....
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...Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing....
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