broadgsa / gatk-protectedView external linksLinks
Official code repository for GATK versions 1.0 through 3.7 (full licensed package). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository
☆146Aug 22, 2018Updated 7 years ago
Alternatives and similar repositories for gatk-protected
Users that are interested in gatk-protected are comparing it to the libraries listed below
Sorting:
- Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk…☆299Aug 22, 2018Updated 7 years ago
- Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead☆32Aug 16, 2017Updated 8 years ago
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,049Feb 4, 2026Updated last week
- MuTect -- Accurate and sensitive cancer mutation detection☆103Feb 13, 2023Updated 3 years ago
- a lightweight db framework for exploring genetic variation.☆324Apr 28, 2020Updated 5 years ago
- Assembly Based ReAligner☆74May 24, 2018Updated 7 years ago
- iCAGES (integrated CAncer GEnome Score) is an effective tool for prioritizing cancer driver genes for a patient☆14Aug 18, 2022Updated 3 years ago
- A Framework to call Structural Variants from NGS based datasets☆22Jan 22, 2018Updated 8 years ago
- Official code repository for GATK versions 4 and up☆1,907Updated this week
- Tools for working with SAM/BAM data☆605Dec 22, 2024Updated last year
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆331May 27, 2025Updated 8 months ago
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,026Aug 24, 2024Updated last year
- Python bindings to minimap2☆16Sep 18, 2017Updated 8 years ago
- C++ API & command-line toolkit for working with BAM data☆429May 18, 2025Updated 8 months ago
- Course material for the de novo assembly part of the INF-BIO9120 course at Univ. of Oslo Fall 2013☆37Oct 1, 2013Updated 12 years ago
- Strelka2 germline and somatic small variant caller☆389Dec 29, 2021Updated 4 years ago
- A flexible framework for rapid genome analysis and interpretation☆319Oct 18, 2022Updated 3 years ago
- A collection of utilities for working with next generation (MPS) sequencing data in Groovy☆15Updated this week
- ☆10Jun 21, 2015Updated 10 years ago
- Tools for early stage alignment file processing☆95Mar 12, 2019Updated 6 years ago
- Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing☆133Jan 27, 2020Updated 6 years ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆862Updated this week
- A Java API for high-throughput sequencing data (HTS) formats.☆294Jan 13, 2026Updated last month
- lumpy: a general probabilistic framework for structural variant discovery☆337Jun 7, 2022Updated 3 years ago
- samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.☆238Aug 11, 2021Updated 4 years ago
- Haplotype VCF comparison tools☆455Dec 7, 2023Updated 2 years ago
- BIC@MSKCC Variants Pipeline☆23Mar 28, 2023Updated 2 years ago
- Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.☆285Dec 19, 2022Updated 3 years ago
- a wee tool for random access into BGZF files.☆86May 10, 2018Updated 7 years ago
- Gene orthologs for model organisms in a tidy data format☆14Sep 29, 2022Updated 3 years ago
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,839Updated this week
- Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data☆213May 14, 2020Updated 5 years ago
- Reads simulator☆283Sep 3, 2021Updated 4 years ago
- A simple tool for extracting reads from Oxford Nanopore fast5 files☆26Sep 4, 2017Updated 8 years ago
- Thousand Variant Callers Project Repository☆73Oct 17, 2019Updated 6 years ago
- Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …☆176Jan 7, 2020Updated 6 years ago
- ☆20Sep 22, 2015Updated 10 years ago
- Isaac Genome Alignment Software☆36Apr 7, 2015Updated 10 years ago
- A Linear Discriminant Analysis Effect Size (LEfSe) wrapper.☆26Feb 2, 2017Updated 9 years ago