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
  ☆551Updated 3 months ago
• nextflow-io / awesome-nextflow
  A curated list of nextflow based pipelines
  ☆609Updated 4 months ago
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,137Updated this week
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,391Updated this week
• shenwei356 / seqkit
  A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  ☆1,482Updated 2 weeks ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆876Updated 9 months ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,512Updated 5 months ago
• jdidion / biotools
  A list of useful bioinformatics resources
  ☆618Updated 6 months ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆1,007Updated 8 months ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆708Updated 7 months ago
• chapmanb / bcbb
  Incubator for useful bioinformatics code, primarily in Python and R
  ☆635Updated 9 months ago
• bcbio / bcbio-nextgen
  Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
  ☆1,019Updated last year
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆510Updated last week
• kblin / ncbi-genome-download
  Scripts to download genomes from the NCBI FTP servers
  ☆1,046Updated 3 months ago
• tseemann / prokka
  Rapid prokaryotic genome annotation
  ☆941Updated last year
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆847Updated last year
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆742Updated 3 months ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆513Updated last month
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆852Updated 5 months ago
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆813Updated 4 months ago
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆751Updated 2 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆552Updated 2 weeks ago
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆1,050Updated 4 years ago
• crazyhottommy / bioinformatics-one-liners
  Bioinformatics one liners from Ming Tang
  ☆495Updated 5 years ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆519Updated 2 months ago
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆871Updated last week
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆703Updated 2 weeks ago
• cmdcolin / awesome-genome-visualization
  A list of interesting genome browser and genome visualization programs
  ☆1,023Updated this week
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆847Updated last year
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆501Updated last week