Alternatives and similar repositories for htsjdk

Users that are interested in htsjdk are comparing it to the libraries listed below

• broadgsa / gatk
  Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk…
  ☆299Updated 7 years ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆515Updated last month
• fulcrumgenomics / fgbio
  Tools for working with genomic and high throughput sequencing data.
  ☆350Updated last week
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆500Updated 2 months ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆331Updated 7 months ago
• pcingola / SnpEff
  ☆299Updated last month
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆322Updated 3 years ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆429Updated 8 months ago
• amplab / snap
  Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
  ☆297Updated 4 months ago
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆603Updated last year
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆280Updated 8 months ago
• jts / sga
  de novo sequence assembler using string graphs
  ☆243Updated 6 years ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆208Updated 4 years ago
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆712Updated this week
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆336Updated 3 years ago
• hartwigmedical / hmftools
  Various algorithms for analysing genomics data
  ☆262Updated this week
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆394Updated 4 months ago
• AstraZeneca-NGS / VarDictJava
  VarDict Java port
  ☆138Updated 2 years ago
• arq5x / gemini
  a lightweight db framework for exploring genetic variation.
  ☆323Updated 5 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆357Updated 8 months ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆455Updated 2 years ago
• bcgsc / abyss
  Assemble large genomes using short reads
  ☆329Updated 9 months ago
• lh3 / wgsim
  Reads simulator
  ☆283Updated 4 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆204Updated 4 years ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆318Updated 3 years ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆389Updated 4 years ago
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆160Updated 3 years ago
• lindenb / jbwa
  Java Bindings (JNI) for bwa
  ☆20Updated 9 years ago
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆523Updated last week
• vcflib / vcflib
  C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
  ☆666Updated 2 months ago