☆306Mar 9, 2026Updated last month
Alternatives and similar repositories for SnpEff
Users that are interested in SnpEff are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆546Apr 13, 2026Updated 3 weeks ago
- This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…☆861Apr 7, 2026Updated 3 weeks ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆514Feb 26, 2026Updated 2 months ago
- Annotation and Ranking of Structural Variation☆293Apr 16, 2026Updated 2 weeks ago
- bedtools - the swiss army knife for genome arithmetic☆1,030Mar 11, 2025Updated last year
- 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.
- Official code repository for GATK versions 4 and up☆1,942Updated this week
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆847Apr 24, 2026Updated last week
- Copy number variant detection from targeted DNA sequencing☆606Updated this week
- structural variant calling and genotyping with existing tools, but, smoothly.☆264Jun 17, 2024Updated last year
- ClassifyCNV: a tool for clinical annotation of copy-number variants☆73Jun 26, 2023Updated 2 years ago
- pbsv - PacBio structural variant (SV) calling and analysis tools☆166Feb 26, 2025Updated last year
- Synteny and Rearrangement Identifier☆463Mar 17, 2026Updated last month
- lumpy: a general probabilistic framework for structural variant discovery☆342Feb 22, 2026Updated 2 months ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,166Apr 25, 2026Updated last week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,731Mar 22, 2025Updated last year
- annotate a VCF with other VCFs/BEDs/tabixed files☆401Aug 30, 2025Updated 8 months ago
- Mummer alignment tool☆558Feb 4, 2025Updated last year
- Structural variant and indel caller for mapped sequencing data☆463Oct 11, 2025Updated 6 months ago
- Structural variant toolkit for VCFs☆407Mar 21, 2026Updated last month
- Tools for working with SAM/BAM data☆610Dec 22, 2024Updated last year
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆335May 27, 2025Updated 11 months ago
- Long read based human genomic structural variation detection with cuteSV☆286Mar 26, 2026Updated last month
- Structural variation caller using third generation sequencing☆651Apr 2, 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.
- A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.☆554May 15, 2025Updated 11 months ago
- A Variant Call Format reader for Python.☆418Sep 22, 2023Updated 2 years ago
- Toolset for SV simulation, comparison and filtering☆416Dec 1, 2023Updated 2 years ago
- Read-based phasing of genomic variants, also called haplotype assembly☆415Dec 31, 2025Updated 4 months ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,351Apr 24, 2026Updated last week
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,061Apr 25, 2026Updated last week
- Toolkit for processing sequences in FASTA/Q formats☆1,538Jun 1, 2025Updated 11 months ago
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆240Aug 11, 2021Updated 4 years ago
- Documentation for the ANNOVAR software☆250Jul 30, 2025Updated 9 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.
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆865Apr 20, 2026Updated 2 weeks ago
- Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling☆358Apr 27, 2026Updated last week
- The next version of bwa-mem☆830Oct 15, 2025Updated 6 months ago
- Jasmine: SV Merging Across Samples☆251Dec 20, 2024Updated last year
- Structural variation and indel detection by local assembly☆255Updated this week
- Variant calling and somatic mutation/CNV detection for next-generation sequencing data☆167Mar 28, 2023Updated 3 years ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆272Mar 15, 2026Updated last month