Alternatives and similar repositories for picard

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

• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆998Updated 6 months ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆869Updated 7 months ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆781Updated 2 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆510Updated last week
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆743Updated 2 weeks ago
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆700Updated last week
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,491Updated 3 months ago
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆842Updated 3 months ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,354Updated this week
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆829Updated last year
• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,782Updated this week
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆689Updated 2 weeks ago
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆506Updated last week
• ncbi / sra-tools
  SRA Tools
  ☆1,255Updated this week
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆692Updated last week
• 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…
  ☆851Updated this week
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆512Updated 2 weeks ago
• lh3 / bwa
  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
  ☆1,654Updated 5 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆754Updated last month
• samtools / htslib
  C library for high-throughput sequencing data formats
  ☆877Updated last week
• bcbio / bcbio-nextgen
  Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
  ☆1,014Updated last year
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆534Updated this week
• lh3 / minimap2
  A versatile pairwise aligner for genomic and spliced nucleotide sequences
  ☆2,033Updated last week
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆734Updated last month
• 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.
  ☆534Updated 4 months ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆872Updated 4 months ago
• broadinstitute / gatk
  Official code repository for GATK versions 4 and up
  ☆1,852Updated this week
• BioContainers / containers
  Bioinformatics containers
  ☆747Updated last week
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆442Updated last year
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆823Updated 2 weeks ago