1887

Abstract

Rapidly 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.

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2016-04-29
2019-09-22
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References

  1. Capella-Gutiérrez S., Silla-Martínez J. M., Gabaldón T.. 2009; trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics25:1972–1973 Available at:http://bioinformatics.oxfordjournals.org/cgi/content/long/25/15/1972 [CrossRef][PubMed]
    [Google Scholar]
  2. Chang C. C., Chow C. C., Tellier L. C. A. M., Vattikuti S., Purcell S. M., Lee J. J.. 2015; Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience4:7 Available athttp://www.gigasciencejournal.com/content/4/1/7 [CrossRef]
    [Google Scholar]
  3. Chewapreecha C., Harris S. R., Croucher N. J., Turner C., Marttinen P., Cheng L., Pessia A., Aanensen D. M., Mather A. E., other authors. 2014; Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet46:305–309 [CrossRef][PubMed]
    [Google Scholar]
  4. Danecek P., Auton A., Abecasis G., Albers C. A., Banks E., DePristo M. A., Handsaker R. E., Lunter G., Marth G. T., other authors. 2011; The variant call format and VCF tools. Bioinformatics27:2156–2158 Available athttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3137218&tool=pmcentrez&rendertype=abstract [CrossRef][PubMed]
    [Google Scholar]
  5. Edgar R. C.. 2004; MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res32:1792–1797 Available athttp://www.ncbi.nlm.nih.gov/pubmed/15034147 [CrossRef][PubMed]
    [Google Scholar]
  6. Felsenstein J.. 1989; Phylip: Phylogeny inference package (version 3.2). Cladistics5:164–166 Available athttp://evolution.genetics.washington.edu/phylip/faq.html#citation
    [Google Scholar]
  7. Katoh K., Standley D. M.. 2013; MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol30:772–780 Available athttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3603318&tool=pmcentrez&rendertype=abstract [CrossRef][PubMed]
    [Google Scholar]
  8. Lindenbaum P.. 2015; JVarkit: java-based utilities for Bioinformatics. Figshare Available at http://dx.doi.org/10.6084/m9.figshare.1425030
    [Google Scholar]
  9. Lischer H. E., Excoffier L.. 2012; Pgdspider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics28:298–299 Available athttp://www.ncbi.nlm.nih.gov/pubmed/22110245 [CrossRef][PubMed]
    [Google Scholar]
  10. Löytynoja A.. 2014; Phylogeny-aware alignment with PRANK. Methods Mol Biol1079:155–170 Available athttp://europepmc.org/abstract/MED/24170401 [CrossRef][PubMed]
    [Google Scholar]
  11. Nasser W.. 2014; Evolutionary pathway to increased virulence and epidemic group A streptococcus disease derived from 3,615 genome sequences. National Academy of Sciences of the United States of America111:E1768–1776 Available athttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4035937&tool=pmcentrez&rendertype=abstract
    [Google Scholar]
  12. Price M. N., Dehal P. S., Arkin A. P.. 2010; Fasttree 2-approximately maximum-likelihood trees for large alignments. plos one, 5, p.e9490. Available athttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2835736&tool=pmcentrez&rendertype=abstract
  13. Stamatakis A.. 2014; Raxml version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics30:1312–1313 [CrossRef][PubMed]
    [Google Scholar]
  14. Sudmant P. H., Rausch T., Gardner E. J., Handsaker R. E., Abyzov A., Huddleston J., Zhang Y., Ye K., Jun G., Korbel J. O.. 1000 Genomes Project Consortium 2015; An integrated map of structural variation in 2,504 human genomes. Nat New Biol526:75–81 Available athttp://dx.doi.org/10.1038/nature15394 [CrossRef][PubMed]
    [Google Scholar]
  15. Swofford D. L.. 2002; paup*: Phylogenetic analysis using parsimony (and other methods), version 4. Sunderland, MA: Sinauer Associates;
  16. Thompson J. D., Gibson T. J., Higgins D. G.. 2002; Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics Available athttp://www.ncbi.nlm.nih.gov/pubmed/18792934
    [Google Scholar]
  17. Wong V. K., Baker S., Pickard D. J., Parkhill J., Page A. J., Feasey N. A., Kingsley R. A., Thomson N. R., Keane J. A., Dougan G.. 2015; Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nat Genet47:632–639 Available athttp://www.ncbi.nlm.nih.gov/pubmed/25961941 [CrossRef][PubMed]
    [Google Scholar]
  18. Wong, V & Holt K. (2016). Figshare: https://dx.doi.org/10.6084/m9.figshare.2067249.v1
  19. Parkhill, J. (2001). Genbank accession number AL513382.
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