SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
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 effici...
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| Veröffentlicht in: | Microbial genomics Jg. 2; H. 4; S. e000056 |
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| Hauptverfasser: | , , , , , , |
| Format: | Journal Article |
| Sprache: | Englisch |
| Veröffentlicht: |
England
Microbiology Society
01.04.2016
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| ISSN: | 2057-5858, 2057-5858 |
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| 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. |
|---|---|
| AbstractList | 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. 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. 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.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. 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 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. is implemented in C and is available under the open source license GNU GPL version 3. |
| Author | Page, Andrew J. Soares, Jorge Seemann, Torsten Harris, Simon R. Keane, Jacqueline A. Taylor, Ben Delaney, Aidan J. |
| Author_xml | – sequence: 1 givenname: Andrew J. surname: Page fullname: Page, Andrew J. organization: 1 Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK – sequence: 2 givenname: Ben surname: Taylor fullname: Taylor, Ben organization: 1 Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK – sequence: 3 givenname: Aidan J. surname: Delaney fullname: Delaney, Aidan J. organization: 2 Computing, Engineering and Mathematics, University of Brighton, Moulsecoomb, Brighton, BN2 4GJ, UK – sequence: 4 givenname: Jorge surname: Soares fullname: Soares, Jorge organization: 1 Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK – sequence: 5 givenname: Torsten surname: Seemann fullname: Seemann, Torsten organization: 3 Victorian Life Sciences Computation Initiative, The University of Melbourne, Parkville, Australia – sequence: 6 givenname: Jacqueline A. surname: Keane fullname: Keane, Jacqueline A. organization: 1 Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK – sequence: 7 givenname: Simon R. surname: Harris fullname: Harris, Simon R. organization: 1 Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28348851$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1093/bioinformatics/btp348 10.1038/ng.3281 10.1093/bioinformatics/btr642 10.1073/pnas.1403138111 10.1186/s13742-015-0047-8 10.1038/nature15394 10.1007/978-1-62703-646-7_10 10.1093/bioinformatics/btr330 10.1093/nar/gkh340 10.1093/bioinformatics/btu033 10.1038/ng.2895 10.1093/molbev/mst010 |
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| References | R2 Price (R16) 2010 R3 R4 Swofford (R19) 2002 R5 Lindenbaum (R10) 2015 R6 Nasser (R13) 2014; 111 R9 Thompson (R20) 2002 B1 R21 B2 B3 R12 R11 R18 R17 Felsenstein (R7) 1989; 5 |
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| Title | SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments |
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