broadinstitute / picardLinks
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
☆1,043Updated this week
Alternatives and similar repositories for picard
Users that are interested in picard are comparing it to the libraries listed below
Sorting:
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆712Updated this week
- bedtools - the swiss army knife for genome arithmetic☆1,018Updated 10 months ago
- The next version of bwa-mem☆805Updated 2 months ago
- Graph-based alignment (Hierarchical Graph FM index)☆521Updated 4 months ago
- Java utilities for Bioinformatics☆513Updated last month
- A fast and sensitive gapped read aligner☆763Updated last month
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆855Updated last year
- A single molecule sequence assembler for genomes large and small.☆695Updated last month
- Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing☆529Updated last week
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,817Updated 3 weeks ago
- Specifications of SAM/BAM and related high-throughput sequencing file formats☆695Updated 2 months ago
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆516Updated last month
- 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…☆874Updated 2 weeks ago
- MACS -- Model-based Analysis of ChIP-Seq☆765Updated last month
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,402Updated last week
- A quality control analysis tool for high throughput sequencing data☆564Updated this week
- Trinity RNA-Seq de novo transcriptome assembly☆879Updated 11 months ago
- C library for high-throughput sequencing data formats☆900Updated 3 weeks ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆860Updated 7 months ago
- Tools for working with SAM/BAM data☆601Updated last year
- Official code repository for GATK versions 4 and up☆1,899Updated this week
- Transcript assembly and quantification for RNA-Seq☆477Updated 2 weeks ago
- Toolkit for processing sequences in FASTA/Q formats☆1,517Updated 7 months ago
- Tools to process and analyze deep sequencing data.☆751Updated 5 months ago
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,688Updated 9 months ago
- A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.☆545Updated 7 months ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆499Updated 2 months ago
- A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…☆536Updated 4 months ago
- This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…☆836Updated 3 weeks ago
- Scripts to download genomes from the NCBI FTP servers☆1,055Updated 5 months ago