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…
  ☆294Updated 6 years ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆424Updated 2 weeks ago
• fulcrumgenomics / fgbio
  Tools for working with genomic and high throughput sequencing data.
  ☆329Updated this week
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆470Updated last month
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆500Updated last week
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆369Updated 3 years ago
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆588Updated 5 months ago
• pcingola / SnpEff
  ☆277Updated 3 months ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆377Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆317Updated 3 years ago
• hartwigmedical / hmftools
  Various algorithms for analysing genomics data
  ☆229Updated this week
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆201Updated 4 years ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆318Updated last week
• lh3 / wgsim
  Reads simulator
  ☆276Updated 3 years ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆594Updated last month
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆327Updated 2 years ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆432Updated last year
• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆398Updated 8 months ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆756Updated 10 months ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆337Updated last month
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆502Updated 6 months ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆268Updated 2 weeks ago
• nextflow-io / patterns
  A curated collection of Nextflow implementation patterns
  ☆359Updated last year
• jts / sga
  de novo sequence assembler using string graphs
  ☆240Updated 5 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆543Updated 10 months ago
• AstraZeneca-NGS / VarDictJava
  VarDict Java port
  ☆134Updated last year
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆258Updated 3 months ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆196Updated 4 years ago
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆679Updated last week
• amplab / snap
  Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
  ☆290Updated last month