Alternatives and similar repositories for hail:

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

• broadinstitute / gatk
  Official code repository for GATK versions 4 and up
  ☆1,769Updated this week
• projectglow / glow
  An open-source toolkit for large-scale genomic analysis
  ☆273Updated this week
• 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
• bcbio / bcbio-nextgen
  Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
  ☆996Updated 5 months ago
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆658Updated this week
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,267Updated last week
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆467Updated last 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.
  ☆995Updated 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…
  ☆808Updated last week
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆803Updated this week
• samtools / htslib
  C library for high-throughput sequencing data formats
  ☆830Updated last week
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆788Updated 8 months ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆492Updated last week
• samtools / htsjdk
  A Java API for high-throughput sequencing data (HTS) formats.
  ☆286Updated this week
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆670Updated this week
• broadinstitute / cromwell
  Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale product…
  ☆1,009Updated this week
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆959Updated last month
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆421Updated last year
• samtools / bcftools
  This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…
  ☆706Updated this week
• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,678Updated last week
• BioContainers / containers
  Bioinformatics containers
  ☆705Updated last month
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆692Updated 2 months ago
• igvteam / igv.js
  Embeddable genomic visualization component based on the Integrative Genomics Viewer
  ☆663Updated this week
• bigdatagenomics / adam
  ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 li…
  ☆1,016Updated last week
• lh3 / bioawk
  BWK awk modified for biological data
  ☆602Updated 2 years ago
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆580Updated 2 months ago
• lh3 / bwa
  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
  ☆1,575Updated 6 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆697Updated this week
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆720Updated this week
• vgteam / vg
  tools for working with genome variation graphs
  ☆1,154Updated this week