What question did this study set out to answer?

To develop and evaluate SNP-sites, an efficient command-line tool designed to rapidly extract single nucleotide polymorphisms from large whole-genome multi-FASTA alignments using modest compute resources.

March 22, 2016Microbial GenomicsOpen Access

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments

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Authors

APAndrew J. PageOrigin Sciences (United Kingdom)BTBen TaylorUniversity of Oxford ADAidan DelaneyNational University of Ireland, Maynooth

Discussion

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Implication

Software evaluation demonstrates rapid, low-memory extraction of single nucleotide polymorphisms from large bacterial alignments, indicating improved scalability for standard computing hardware.

Key Points

To develop and evaluate SNP-sites, an efficient command-line tool designed to rapidly extract single nucleotide polymorphisms from large whole-genome multi-FASTA alignments using modest compute resources.
Engineered an open-source tool implemented in C to parse multi-FASTA alignment files and output polymorphic positions into multiple downstream formats.
Benchmarked runtime and memory requirements on a single CPU core using an 8.3 GB alignment dataset consisting of 1,842 taxa and 22,618 sites across more than 20 operating systems.
Extracted all single nucleotide polymorphisms from the 8.3 GB benchmark alignment in 267 seconds while consuming 59 MB of RAM on 1 CPU core.
Achieved cross-platform deployment across more than 20 operating systems via Debian and Homebrew package managers under the GNU GPLv3 license.

Cite This Study

Page et al. (2016) studied this question.

synapsesocial.com/papers/69dd50967808b00a4799ca5b https://doi.org/10.1099/mgen.0.000056

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Implication

Software evaluation demonstrates rapid, low-memory extraction of single nucleotide polymorphisms from large bacterial alignments, indicating improved scalability for standard computing hardware.