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☆344Feb 22, 2026Updated 4 months ago
- Tools for working with SAM/BAM data☆613Dec 22, 2024Updated last year
- a lightweight db framework for exploring genetic variation.☆329Apr 28, 2020Updated 6 years ago
- Structural variant and indel caller for mapped sequencing data☆468Oct 11, 2025Updated 9 months ago
- Bayesian genotyper for structural variants☆136Apr 13, 2026Updated 3 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.
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆527Updated this week
- Canvas - Copy number variant (CNV) calling from DNA sequencing data☆129Apr 20, 2026Updated 3 months ago
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆242Aug 11, 2021Updated 4 years ago
- VarDict☆204Jan 5, 2024Updated 2 years ago
- A tool set for short variant discovery in genetic sequence data.☆206May 4, 2021Updated 5 years ago
- tools for adding mutations to existing .bam files, used for testing mutation callers☆251Oct 18, 2024Updated last year
- Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data☆177Aug 22, 2024Updated last year
- a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads☆235Feb 17, 2022Updated 4 years ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆682Mar 20, 2026Updated 4 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☆1,029Aug 24, 2024Updated last year
- 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...)☆2,400Jul 10, 2026Updated last week
- Personal Cancer Genome Reporter (PCGR)☆281Jul 12, 2026Updated last 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☆865May 2, 2026Updated 2 months ago
- Plot structural variant signals from many BAMs and CRAMs☆571Jul 13, 2024Updated 2 years ago
- Haplotype VCF comparison tools☆471Dec 7, 2023Updated 2 years ago
- The next version of bwa-mem☆851Oct 15, 2025Updated 9 months ago
- Structural variation and indel detection by local assembly☆256Updated this 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)☆1,758Jun 20, 2026Updated last month
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆876Apr 20, 2026Updated 3 months ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆406Jun 16, 2026Updated last month
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …☆178Jan 7, 2020Updated 6 years ago
- ☆69Jun 21, 2022Updated 4 years ago
- Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data☆213May 14, 2020Updated 6 years ago
- structural variant calling and genotyping with existing tools, but, smoothly.☆266Jun 17, 2024Updated 2 years ago
- Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec☆13Aug 25, 2020Updated 5 years ago
- The Genome Modeling System installer☆78Jul 10, 2015Updated 11 years ago
- Software program for checking sample matching for NGS data☆141Jun 20, 2024Updated 2 years ago