Alternatives and similar repositories for containers:

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

• jorvis / biocode
  Bioinformatics code libraries and scripts
  ☆518Updated 3 weeks ago
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆989Updated 3 weeks ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,431Updated 6 months ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,270Updated this week
• nextflow-io / awesome-nextflow
  A curated list of nextflow based pipelines
  ☆580Updated 2 years ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆962Updated last month
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆494Updated this week
• jdidion / biotools
  A list of useful bioinformatics resources
  ☆598Updated last year
• OpenGene / fastp
  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
  ☆2,023Updated 3 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆483Updated last year
• bcbio / bcbio-nextgen
  Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
  ☆996Updated 6 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆702Updated this week
• tiagoantao / bioinf-python
  Python for Bioinformatics
  ☆252Updated 4 years ago
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆426Updated this week
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆595Updated 9 months ago
• crazyhottommy / bioinformatics-one-liners
  Bioinformatics one liners from Ming Tang
  ☆462Updated 4 years ago
• kblin / ncbi-genome-download
  Scripts to download genomes from the NCBI FTP servers
  ☆985Updated 7 months ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆850Updated last month
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆764Updated this week
• mdshw5 / pyfaidx
  Efficient pythonic random access to fasta subsequences
  ☆464Updated 4 months ago
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆792Updated 9 months ago
• chapmanb / bcbb
  Incubator for useful bioinformatics code, primarily in Python and R
  ☆616Updated last month
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆808Updated last week
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆777Updated 7 months ago
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆983Updated 3 years ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆430Updated 11 months ago
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆800Updated 2 weeks ago
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆671Updated last week
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆739Updated 7 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆723Updated 2 weeks ago