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 (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers.

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.

Apr 29, 2016 · 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 …

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.

In genetics and bioinformatics, a single-nucleotide polymorphism (SNP / snɪp /; plural SNPs / snɪps /) is a germline substitution of a single nucleotide at a specific position in the genome.

Finds SNP sites from a multi-FASTA alignment file.

Finds SNP sites from a multi-FASTA alignment file. You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

SNP-sites extracts single nucleotide polymorphisms (SNPs) from a multi-FASTA alignment outputs results in multiple formats for downstream analysis. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments.

Mar 22, 2022 · Single nucleotide polymorphisms, frequently called SNPs (pronounced “snips”), are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block, called a nucleotide. For example, a SNP may replace the nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA.

Jan 29, 2016 · 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 (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers.