broadinstitute / gatkLinks
Official code repository for GATK versions 4 and up
☆1,877Updated this week
Alternatives and similar repositories for gatk
Users that are interested in gatk are comparing it to the libraries listed below
Sorting:
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,800Updated 3 weeks ago
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,676Updated 8 months ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,220Updated last month
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,034Updated last week
- bedtools - the swiss army knife for genome arithmetic☆1,007Updated 8 months ago
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,019Updated last year
- SRA Tools☆1,272Updated this week
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,391Updated this week
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆703Updated 2 weeks ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,072Updated last month
- Toolkit for processing sequences in FASTA/Q formats☆1,512Updated 5 months ago
- tools for working with genome variation graphs☆1,256Updated last week
- A fast and sensitive gapped read aligner☆751Updated 2 months ago
- Bioinformatics containers☆762Updated 3 weeks ago
- Trinity RNA-Seq de novo transcriptome assembly☆876Updated 9 months ago
- The next version of bwa-mem☆795Updated last month
- C library for high-throughput sequencing data formats☆889Updated last week
- 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…☆864Updated 2 weeks ago
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆847Updated last year
- RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.☆1,137Updated last week
- Specifications of SAM/BAM and related high-throughput sequencing file formats☆688Updated 2 weeks ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆852Updated 5 months ago
- This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…☆819Updated 2 weeks ago
- MACS -- Model-based Analysis of ChIP-Seq☆759Updated this week
- Cloud-native genomic dataframes and batch computing☆1,037Updated last week
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,482Updated 3 weeks ago
- Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis inclu…☆1,401Updated 2 years ago
- Graph-based alignment (Hierarchical Graph FM index)☆519Updated 2 months ago
- RNAseq analysis notes from Ming Tang☆1,050Updated 4 years ago
- A list of interesting genome browser and genome visualization programs☆1,023Updated last week