Alternatives and similar repositories for htslib

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

• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,799Updated last week
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆747Updated last month
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆789Updated 2 weeks ago
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆689Updated last month
• vcflib / vcflib
  C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
  ☆659Updated this week
• samtools / bcftools
  This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…
  ☆818Updated last week
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆849Updated 5 months ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆1,004Updated 7 months ago
• lh3 / bwa
  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
  ☆1,667Updated 7 months ago
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆841Updated last year
• lh3 / minimap2
  A versatile pairwise aligner for genomic and spliced nucleotide sequences
  ☆2,058Updated 3 weeks ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆514Updated last month
• gmarcais / Jellyfish
  A fast multi-threaded k-mer counter
  ☆516Updated last year
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆595Updated 10 months ago
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆694Updated last month
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,503Updated 5 months ago
• pysam-developers / pysam
  Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight…
  ☆859Updated last month
• seqan / seqan
  SeqAn's official repository.
  ☆496Updated last month
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆447Updated last year
• vcftools / vcftools
  A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
  ☆538Updated 5 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆546Updated last month
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆699Updated last week
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆509Updated 2 weeks ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆490Updated 2 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆470Updated last week
• lh3 / bioawk
  BWK awk modified for biological data
  ☆630Updated 3 years ago
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆646Updated 2 years ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆875Updated 8 months ago
• ablab / spades
  SPAdes Genome Assembler
  ☆874Updated 2 weeks ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆706Updated 6 months ago