GATK is a genomic analysis toolkit focused on variant discovery.
The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling, and to tackle copy number (CNV) and structural variation (SV). In addition to the variant callers themselves, the GATK also includes many utilities to perform related tasks such as processing and quality control of high-throughput sequencing data, and bundles the popular Picard toolkit.
These tools were primarily designed to process exomes and whole genomes generated with Illumina sequencing technology, but they can be adapted to handle a variety of other technologies and experimental designs. And although it was originally developed for human genetics, the GATK has since evolved to handle genome data from any organism, with any level of ploidy.
This is free and open source software.
Website: gatk.broadinstitute.org/hc/en-us
Support: GitHub Code Repository
Developer: Broad Institute, Inc.
License: Apache License 2.0
GATK is written in Java. Learn Java with our recommended free books and free tutorials.
Related Software
| Bioinformatics Tools | |
|---|---|
| Bioconductor | Analysis and comprehension of high-throughput genomic data |
| Biopython | Tools for biological computation written in Python |
| UGENE | Set of integrated bioinformatics software |
| BioPerl | Perl tools for computational molecular biology |
| GROMACS | Versatile package to perform molecular dynamics |
| IGV | High-performance visualization genome browser tool |
| GATK | Genomic analysis toolkit focused on variant discovery |
| BioJava | Provides Java tools for processing biological data |
| InterMine | Integrate biological data sources |
| bedtools | Powerful toolset for genome arithmetic |
| EMBOSS | The European Molecular Biology Open Software Suite |
| BLAST | Algorithm for comparing primary biological sequence information |
| Galaxy | Web-based platform for data-intensive computational research |
| minimap2 | Versatile sequence alignment program |
| Scanpy | Scalable analysis of single-cell gene expression data |
| Jalview | Multiple sequence alignment editing, visualisation and analysis |
| SeqKit | Fast toolkit for manipulating FASTA and FASTQ sequence files |
| samtools | Manipulate next-generation sequencing data |
| MultiQC | Aggregates results from multiple bioinformatics analyses |
| BCFtools | Variant calling and manipulating files in the Variant Call Format |
| Foldseek | Fast searching and comparison of large protein structure datasets |
| FastQC | Quality control tool for high throughput sequence data |
| SPAdes | Versatile toolkit for assembling and analysing sequencing data |
| GenomeTools | Collection of bioinformatics tools |
| AliView | Alignment viewer and editor |
| mothur | Analyze microbial communities |
| Bandage | Visualising de novo assembly graphs |
| cramino | BAM/CRAM quality evaluation |
| abPOA | Adaptive banded Partial Order Alignment |
Read our verdict in the software roundup.
 Explore our carefully curated directory of recommended free and open source software, covering every major software category.The directory forms part of our extensive collection of articles for Linux enthusiasts. It includes hundreds of detailed reviews, together with free and open source alternatives to proprietary software from companies such as Google, Microsoft, Apple, Adobe, IBM, Cisco, Oracle, and Autodesk. LinuxLinks also covers interesting projects worth exploring, Linux-compatible hardware, free programming books and tutorials, and much more. Know a useful free and open source Linux application that we haven’t covered? Tell us about it using our submission form. |
Please read our Comment Policy before commenting.