Alternatives and similar repositories for htslib:

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

• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆739Updated 7 months ago
• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,681Updated this week
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆696Updated 2 months ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆962Updated last month
• samtools / bcftools
  This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…
  ☆710Updated this week
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆671Updated 2 weeks ago
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆808Updated last week
• vcflib / vcflib
  C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
  ☆634Updated 3 months ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆421Updated last year
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆584Updated 7 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆496Updated 3 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆415Updated 2 weeks ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,430Updated 6 months ago
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆670Updated last week
• 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…
  ☆811Updated 3 weeks ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆458Updated this week
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆606Updated 2 years ago
• lh3 / minimap2
  A versatile pairwise aligner for genomic and spliced nucleotide sequences
  ☆1,889Updated 3 months ago
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆470Updated last week
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆578Updated 3 weeks ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,270Updated this week
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆812Updated 6 months ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆494Updated this week
• broadinstitute / picard
  A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
  ☆996Updated last week
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆430Updated 11 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆408Updated 2 months ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆423Updated 7 months ago
• lh3 / minigraph
  Sequence-to-graph mapper and graph generator
  ☆436Updated 9 months ago
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆580Updated 2 months ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆850Updated 3 weeks ago