SNPick¶

Fast, memory-efficient extraction of variable sites from FASTA alignments.

Get started Usage reference View on GitHub

SNPick extracts variable (SNP) sites from whole-genome FASTA alignments. It produces reduced alignments ready for phylogenetic inference with ascertainment-bias correction (ASC) in IQ-TREE and RAxML, and optionally generates VCF files.

Why not snp-sites?

snp-sites works well for small datasets but struggles with large alignments — it loads the whole matrix into memory and scales poorly. SNPick uses a zero-copy, memory-mapped architecture that handles thousands of genomes in seconds with minimal RAM.

What you get¶

Variable sites only

A reduced FASTA with just the informative columns — a drop-in, much smaller input for phylogenetics.
ASC-ready

Constant-site counts (fconst) printed for IQ-TREE's +ASC models, so branch lengths stay unbiased.
Optional VCF

VCF v4.2 with per-sample genotypes, a configurable contig name, alignment-column POS (or ungapped reference coordinates with --ref-coords), and gap/ambiguity handling.
Filter & mask

Per-site missingness / MAC / MAF / allele filters, BED region masking and sample selection — without breaking fconst.
Pipeline-native

gzip & stdin/stdout streaming, PHYLIP/NEXUS output, and a --stats-json sidecar so nothing scrapes stderr.
Built for scale

Zero-copy mmap + parallel, auto-vectorized scan: O(L) memory, thousands of genomes in seconds.

SNPick vs snp-sites¶

	SNPick	snp-sites
Architecture	Zero-copy mmap, parallel scan	Full matrix in memory
250 seqs × 4.4 Mbp	1.72 s, 105 MB	9.38 s, 213 MB
1000 seqs × 4.4 Mbp	10.27 s, 217 MB	killed (OOM)
ASC `fconst` output	Built-in	Not supported
VCF output	Optional	Default
Gap handling	Optional (`-g`)	Default
IUPAC ambiguous	Tracked as ambiguous	Treated as variant

Quick start¶

# Install from Bioconda
conda install -c bioconda snpick

# Extract variable sites
snpick -f alignment.fasta -o snps.fasta

# With a VCF, on 8 threads, quietly
snpick -f alignment.fasta -o snps.fasta --vcf -t 8 -q

Citation¶

If you use SNPick in your research, please cite:

@software{snpick,
  author  = {Ruiz-Rodriguez, Paula and Coscolla, Mireia},
  title   = {SNPick: Fast extraction of variable sites from FASTA alignments},
  url     = {https://github.com/PathoGenOmics-Lab/snpick},
  doi     = {10.5281/zenodo.14191809},
  license = {GPL-3.0}
}

_{Paula Ruiz-Rodriguez and Mireia Coscolla — Institute for Integrative Systems Biology, I²SysBio, University of Valencia-CSIC, Valencia, Spain.}