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
  ☆1,799Updated last week
• lh3 / bwa
  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
  ☆1,667Updated 7 months ago
• OpenGene / fastp
  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
  ☆2,211Updated 2 weeks 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.
  ☆1,033Updated 3 weeks ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,384Updated this week
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆1,004Updated 7 months ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,503Updated 5 months ago
• lh3 / minimap2
  A versatile pairwise aligner for genomic and spliced nucleotide sequences
  ☆2,058Updated 3 weeks ago
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,118Updated 2 weeks ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆875Updated 8 months ago
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆699Updated last week
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆689Updated last month
• BioContainers / containers
  Bioinformatics containers
  ☆758Updated last week
• samtools / htslib
  C library for high-throughput sequencing data formats
  ☆886Updated last week
• griffithlab / rnaseq_tutorial
  Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis inclu…
  ☆1,393Updated 2 years ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆789Updated 2 weeks ago
• bcbio / bcbio-nextgen
  Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
  ☆1,017Updated last year
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆747Updated last month
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆841Updated last year
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆758Updated last week
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆849Updated 5 months ago
• ncbi / sra-tools
  SRA Tools
  ☆1,264Updated last week
• samtools / bcftools
  This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…
  ☆818Updated last week
• alexdobin / STAR
  RNA-seq aligner
  ☆2,067Updated 7 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…
  ☆859Updated last month
• shenwei356 / seqkit
  A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  ☆1,478Updated 2 weeks ago
• hail-is / hail
  Cloud-native genomic dataframes and batch computing
  ☆1,032Updated last week
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆827Updated last year
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆741Updated 3 months ago
• quinlan-lab / applied-computational-genomics
  Applied Computational Genomics Course at UU: Spring 2020
  ☆1,057Updated last year