SNPick
SNPick is a fast and memory-efficient tool designed to extract SNP (Single Nucleotide Polymorphism) sites from large-scale FASTA alignments, taking into consideration IUPAC ambiguous nucleotides. SNP analysis is critical for understanding genetic variation, phylogenetic relationships, and evolutionary biology. SNPick was developed to provide a highly scalable and optimized approach to SNP extraction. Unlike snp-sites, SNPick employs parallel processing and an efficient memory management strategy, making it suitable for very large datasets. This scalability allows users to work with massive alignments, extracting SNPs in a fraction of the time and with significantly lower memory requirements compared to traditional tools.
Basic Information
| Repository | https://github.com/PathoGenOmics-Lab/snpick |
| Documentation | https://github.com/PathoGenOmics-Lab/snpick/blob/main/README.md |
| Main publication (DOI) | 10.5281/zenodo.14191809 view |
| Contact email | paula.ruiz.rodriguez@csic.es |
| Authors/Maintainers | Mireia Coscolla Devis, Paula Ruiz Rodríguez |
| Type of application | Command line pipeline, Conda package |
| Programming languages | Rust |
| Keywords | Omics, Computational Methods, Resources, Genomics, Computational Techniques, Parallel Computing, Variant calling, Molecular evolution, Population genomics, Sequence analysis, Phylogenetic Analysis, Evolutionary rates |
Technical details
| Input file formats | fasta |
| Output file formats | tsv, fasta |
| Software compatibility | Linux, Mac |
| Hardware requirements | |
| Type of containerization | None |
| Wrapper type | None |
| Compatible tools | |
| Funding resource | No funding |
| Funding support |
Statistics
| Unique users (last 12 months) | |
| Unique users (since first release) | |
| Software downloads (last 12 months) | 453 |
| Software downloads (since first release) | 453 |
| Jobs submitted (last 12 months) | |
| Jobs submitted (since first release) | |
| Repository clones (last 12 months) | 2 |
| Repository clones (since first release) | 2 |
| Citations (last 12 months) | <100 (~0 as of 15/10/2026) |
| Citations (since first release) | <100 (0 as of 15/10/2026) |
| Early-stage researcher effort (development) | doctoral candidate |
| Early-stage researcher effort (maintenance) | doctoral candidate |
| Technician-supported effort (development) | |
| Technician-supported effort (maintenance) | |
| Other effort (development) | |
| Other effort (maintenance) | |
| Total effort (development) | |
| Total effort (maintenance) |