A flexible framework for rapid genome analysis and interpretation
☆320Oct 18, 2022Updated 3 years ago
Alternatives and similar repositories for speedseq
Users that are interested in speedseq are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- lumpy: a general probabilistic framework for structural variant discovery☆346Feb 22, 2026Updated 6 months ago
- a lightweight db framework for exploring genetic variation.☆328Apr 28, 2020Updated 6 years ago
- Tools for working with SAM/BAM data☆613Dec 22, 2024Updated last year
- Structural variant and indel caller for mapped sequencing data☆468Oct 11, 2025Updated 10 months ago
- Bayesian genotyper for structural variants☆136Apr 13, 2026Updated 4 months ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆534Updated this week
- Canvas - Copy number variant (CNV) calling from DNA sequencing data☆129Apr 20, 2026Updated 4 months ago
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆243Aug 11, 2021Updated 5 years ago
- VarDict☆204Jan 5, 2024Updated 2 years ago
- A tool set for short variant discovery in genetic sequence data.☆207May 4, 2021Updated 5 years ago
- tools for adding mutations to existing .bam files, used for testing mutation callers☆251Aug 5, 2026Updated 3 weeks ago
- Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data☆178Aug 22, 2024Updated 2 years ago
- a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads☆236Feb 17, 2022Updated 4 years ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆684Mar 20, 2026Updated 5 months ago
- 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.
- De novo assembly based variant calling pipeline for Illumina short reads☆110Nov 30, 2020Updated 5 years ago
- Detect and visualize target mutations by scanning FastQ files directly☆157Feb 10, 2022Updated 4 years ago
- Microassembly based somatic variant caller for NGS data☆154Jun 23, 2022Updated 4 years ago
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,030Aug 24, 2024Updated 2 years ago
- Tools for processing and analyzing structural variants.☆157May 2, 2022Updated 4 years ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆338May 27, 2025Updated last year
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,422Jul 30, 2026Updated last month
- Personal Cancer Genome Reporter (PCGR)☆283Updated this week
- Tools for early stage alignment file processing☆96Mar 12, 2019Updated 7 years ago
- 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.
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆871May 2, 2026Updated 3 months ago
- Plot structural variant signals from many BAMs and CRAMs☆572Jul 13, 2024Updated 2 years ago
- Haplotype VCF comparison tools☆471Dec 7, 2023Updated 2 years ago
- The next version of bwa-mem☆858Oct 15, 2025Updated 10 months ago
- Structural variation and indel detection by local assembly☆258Aug 19, 2026Updated last week
- A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.☆170Apr 18, 2022Updated 4 years ago
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,766Aug 7, 2026Updated 3 weeks ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆877Apr 20, 2026Updated 4 months ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆404Jun 16, 2026Updated 2 months ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- ☆69Jun 21, 2022Updated 4 years ago
- Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …☆178Jan 7, 2020Updated 6 years ago
- Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data☆214May 14, 2020Updated 6 years ago
- Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec☆13Aug 25, 2020Updated 6 years ago
- structural variant calling and genotyping with existing tools, but, smoothly.☆267Jun 17, 2024Updated 2 years ago
- The Genome Modeling System installer☆78Jul 10, 2015Updated 11 years ago
- Software program for checking sample matching for NGS data☆143Jun 20, 2024Updated 2 years ago