Alternatives and similar repositories for gatk

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

• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,819Updated this week
• lh3 / bwa
  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
  ☆1,693Updated 9 months ago
• 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.
  ☆1,045Updated 2 weeks ago
• OpenGene / fastp
  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
  ☆2,262Updated last week
• ncbi / sra-tools
  SRA Tools
  ☆1,292Updated this week
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆1,020Updated 10 months ago
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆712Updated this week
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,408Updated this week
• lh3 / minimap2
  A versatile pairwise aligner for genomic and spliced nucleotide sequences
  ☆2,102Updated last month
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,518Updated 7 months ago
• bcbio / bcbio-nextgen
  Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
  ☆1,024Updated last year
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆695Updated 2 months ago
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆763Updated last month
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆807Updated 3 months ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆880Updated 11 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…
  ☆875Updated last week
• samtools / bcftools
  This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…
  ☆835Updated last month
• BioContainers / containers
  Bioinformatics containers
  ☆769Updated 2 months ago
• shenwei356 / seqkit
  A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  ☆1,498Updated last week
• samtools / htslib
  C library for high-throughput sequencing data formats
  ☆900Updated last month
• hail-is / hail
  Cloud-native genomic dataframes and batch computing
  ☆1,045Updated this week
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆1,063Updated 4 years ago
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆860Updated 7 months ago
• 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.
  ☆546Updated 8 months ago
• cmdcolin / awesome-genome-visualization
  A list of interesting genome browser and genome visualization programs
  ☆1,042Updated this week
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆523Updated last week
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆767Updated last month
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,179Updated last week
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆854Updated last year
• quinlan-lab / applied-computational-genomics
  Applied Computational Genomics Course at UU: Spring 2020
  ☆1,071Updated last year