Alternatives and similar repositories for bcftools:

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

• samtools / htslib
  C library for high-throughput sequencing data formats
  ☆847Updated last week
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆751Updated 9 months ago
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆823Updated 2 months ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆979Updated last month
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆428Updated last year
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆501Updated last year
• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,722Updated last week
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆674Updated 3 weeks ago
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆475Updated 2 weeks ago
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆674Updated last week
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆711Updated 4 months ago
• lh3 / bioawk
  BWK awk modified for biological data
  ☆615Updated 2 years ago
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆674Updated last week
• 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.
  ☆524Updated last year
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆591Updated 3 weeks ago
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆784Updated 2 weeks ago
• vcflib / vcflib
  C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
  ☆643Updated this week
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆463Updated last week
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆826Updated this week
• nanopore-wgs-consortium / NA12878
  Data and analysis for NA12878 genome on nanopore
  ☆389Updated 2 years ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆375Updated last year
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆438Updated last year
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,455Updated 8 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆418Updated 2 weeks ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆498Updated last week
• usadellab / Trimmomatic
  ☆242Updated 11 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆616Updated 11 months ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆501Updated last month
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆501Updated 5 months ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆368Updated 3 years ago