Alternatives and similar repositories for bcftools

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

• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆513Updated this week
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆798Updated last month
• 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.
  ☆539Updated 6 months ago
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆856Updated 6 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆557Updated 2 weeks ago
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆755Updated 2 weeks ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆1,013Updated 9 months ago
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆690Updated last month
• samtools / htslib
  C library for high-throughput sequencing data formats
  ☆892Updated last week
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆706Updated this 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…
  ☆870Updated 2 weeks ago
• vcflib / vcflib
  C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
  ☆662Updated last month
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆453Updated 2 years ago
• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,808Updated 2 weeks ago
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆695Updated 3 weeks ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆626Updated last month
• lh3 / bioawk
  BWK awk modified for biological data
  ☆633Updated 3 years ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆513Updated last week
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆853Updated 2 weeks ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,515Updated 6 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆520Updated 3 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆456Updated last year
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆763Updated 2 weeks ago
• ncbi / sra-tools
  SRA Tools
  ☆1,282Updated this week
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆472Updated 3 weeks ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆883Updated 7 months ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,397Updated this week
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆747Updated 4 months ago
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆597Updated 11 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆438Updated 4 months ago