Simple pileup-based variant caller
☆95Apr 25, 2025Updated last year
Alternatives and similar repositories for minipileup
Users that are interested in minipileup are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Everything but the kitchen sink☆13Feb 6, 2025Updated last year
- base-accurate DNA sequence alignments using WFA and mashmap3☆224Updated this week
- Constructing a pangenome gene graph☆212Aug 11, 2025Updated last year
- Pairwise whole genome aligner☆244Sep 4, 2026Updated 3 weeks ago
- Wavefront alignment algorithm (WFA) in Golang☆33Aug 21, 2026Updated last month
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Correcting errors in noisy long reads using variation graphs☆53Nov 17, 2022Updated 3 years ago
- implicit pangenome graph☆114Updated this week
- Parsing and evaluating gene annotation and spliced alignment☆29Jul 22, 2025Updated last year
- MEMO: MEM-based pangenome indexing for k-mer queries☆20Jun 11, 2024Updated 2 years ago
- Transfer HiFi read mappings from their own assembly contigs to a standard reference☆40Dec 30, 2025Updated 8 months ago
- Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome☆100Jan 28, 2026Updated 7 months ago
- A multiscale pangenome browser☆36Jul 18, 2026Updated 2 months ago
- Lightweight mosaic/somatic SV caller for long reads (WIP)☆36Oct 27, 2025Updated 11 months ago
- plane sweep filtering genome alignments☆24Updated this week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Open Human Genome Library☆69Dec 22, 2025Updated 9 months ago
- Whole Genome Alignment Tools☆223Nov 6, 2025Updated 10 months ago
- bioinformatics toolkit in rust☆108Aug 16, 2026Updated last month
- a precise pangenome browser combining linear and graph-based pan-genome☆13Jul 16, 2024Updated 2 years ago
- ☆43Oct 6, 2025Updated 11 months ago
- ☆18Jan 29, 2025Updated last year
- Scoring GT/AG sites for improving spliced alignment☆59Nov 10, 2025Updated 10 months ago
- Variant Calling for the HPRC2☆17May 26, 2026Updated 4 months ago
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- ☆42May 19, 2025Updated last year
- Copy number caller for long read data including SNV utilization☆71Mar 31, 2025Updated last year
- Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions☆38Apr 28, 2026Updated 4 months ago
- SRF: Satellite Repeat Finder☆109Jan 8, 2024Updated 2 years ago
- BWT construction and search☆131Aug 30, 2026Updated 3 weeks ago
- LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads☆111Jun 25, 2026Updated 3 months ago
- GFA insert into GenomicSQLite☆49Jun 7, 2021Updated 5 years ago
- Genotyping lots of samples with big pangenomes☆11Oct 30, 2025Updated 10 months ago
- Evaluating genome assemblies☆127Mar 3, 2026Updated 6 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Genome size estimation from long read overlaps☆97Sep 8, 2026Updated 2 weeks ago
- An experimental tool to estimate the similarity between all pairs of contigs☆40Apr 12, 2021Updated 5 years ago
- Successor of bwa-mem for short-read alignment☆350Aug 13, 2026Updated last month
- Mumemto: multi-MUM and MEM finding across pangenomes☆137Updated this week
- Error correction of long reads☆16Jan 30, 2026Updated 7 months ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆145Aug 24, 2025Updated last year
- A program for assessing the T2T genome continuity and completeness☆97Sep 8, 2026Updated 2 weeks ago