samtools / htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
☆286Updated this week
Alternatives and similar repositories for htsjdk:
Users that are interested in htsjdk are comparing it to the libraries listed below
- Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk…☆294Updated 6 years ago
- Java utilities for Bioinformatics☆497Updated last week
- Tools for working with genomic and high throughput sequencing data.☆325Updated this week
- Count bases in BAM/CRAM files☆315Updated 3 years ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆462Updated last month
- C++ API & command-line toolkit for working with BAM data☆422Updated 9 months ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆315Updated 10 months ago
- ☆268Updated 2 months ago
- Haplotype VCF comparison tools☆426Updated last year
- annotate a VCF with other VCFs/BEDs/tabixed files☆372Updated last year
- GRIDSS: the Genomic Rearrangement IDentification Software Suite☆268Updated last year
- Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls☆203Updated 4 years ago
- Structural variation caller using third generation sequencing☆587Updated this week
- lumpy: a general probabilistic framework for structural variant discovery☆323Updated 2 years ago
- Various algorithms for analysing genomics data☆222Updated this week
- Graph-based alignment (Hierarchical Graph FM index)☆499Updated 5 months ago
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆673Updated this week
- Tools for working with SAM/BAM data☆583Updated 3 months ago
- A flexible framework for rapid genome analysis and interpretation☆316Updated 2 years ago
- Transcript assembly and quantification for RNA-Seq☆433Updated this week
- Text Only Genome Viewer!☆219Updated last week
- STAR-Fusion codebase☆239Updated 2 months ago
- Pilon is an automated genome assembly improvement and variant detection tool☆357Updated 3 years ago
- Documentation for the ANNOVAR software☆242Updated 3 weeks ago
- BEDOPS: high-performance genomic feature operations☆328Updated last week
- Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data☆290Updated last month
- A quality control analysis tool for high throughput sequencing data☆494Updated last year
- cython + htslib == fast VCF and BCF processing☆394Updated 7 months ago
- Assemble large genomes using short reads☆317Updated 3 weeks ago
- Reads simulator☆274Updated 3 years ago