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dc.contributor.authorPage, AJ
dc.contributor.authorTaylor, B
dc.contributor.authorDelaney, AJ
dc.contributor.authorSoares, J
dc.contributor.authorSeemann, T
dc.contributor.authorKeane, JA
dc.contributor.authorHarris, SR
dc.date.accessioned2021-02-05T01:24:21Z
dc.date.available2021-02-05T01:24:21Z
dc.date.issued2016-04-01
dc.identifier.citationPage, A. J., Taylor, B., Delaney, A. J., Soares, J., Seemann, T., Keane, J. A. & Harris, S. R. (2016). SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. MICROBIAL GENOMICS, 2 (4), https://doi.org/10.1099/mgen.0.000056.
dc.identifier.issn2057-5858
dc.identifier.urihttp://hdl.handle.net/11343/260386
dc.description.abstractRapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. Extracting single nucleotide polymorphisms (SNPs) from a large whole genome alignment is now a routine task, but existing tools have failed to scale efficiently with the increased size of studies. These tools are slow, memory inefficient and are installed through non-standard procedures. We present SNP-sites which can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1842 taxa, 22 618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. It is easy to install through the Debian and Homebrew package managers, and has been successfully tested on more than 20 operating systems. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.
dc.languageEnglish
dc.publisherMICROBIOLOGY SOC
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleSNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
dc.typeJournal Article
dc.identifier.doi10.1099/mgen.0.000056
melbourne.affiliation.departmentMicrobiology and Immunology
melbourne.affiliation.facultyMedicine, Dentistry & Health Sciences
melbourne.source.titleMicrobial Genomics
melbourne.source.volume2
melbourne.source.issue4
dc.rights.licenseCC BY
melbourne.elementsid1061227
melbourne.contributor.authorSeemann, Torsten
dc.identifier.eissn2057-5858
melbourne.accessrightsOpen Access


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