Alternatives and similar repositories for toolshed

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

• xguse / blacktie
  Blacktie: a streamlined interface to the popular tophat/cufflinks RNA-seq pipeline
  ☆26Updated 9 years ago
• karel-brinda / smbl
  SMBL - SnakeMake Bioinformatics Library. Automatic installation of bioinformatics software in your SnakeMake pipelines.
  ☆23Updated 7 years ago
• iqbal-lab / cortex
  reference free variant assembly
  ☆33Updated last year
• nanoporetech / minimappy
  Python bindings to minimap2
  ☆16Updated 7 years ago
• jrderuiter / geneviz
  Library for visualising genomic features in Python.
  ☆15Updated 8 years ago
• COMBINE-lab / RapClust
  Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes
  ☆31Updated last year
• wtsi-svi / ReadServer
  Using reference-free compressed data structures to analyse thousands of human genomes (1000 Genomes ReadServer)
  ☆14Updated 7 years ago
• camillescott / shmlast
  blast, shmlast
  ☆22Updated 4 years ago
• tseemann / homebrew-bioinformatics-linux
  Homebrew formulae for bioinformatics software only available for Linux
  ☆27Updated 5 years ago
• koelling / dnacol
  Color DNA/RNA bases in terminal output
  ☆21Updated 7 years ago
• alexpreynolds / soda
  Python-based UCSC genome browser snapshot-taker and gallery-maker
  ☆12Updated last year
• fomightez / sequencework
  programs and scripts, mainly python, for analyses related to nucleic or protein sequences
  ☆24Updated 2 months ago
• inutano / docker-ngs-tools
  A catalogue of docker images for NGS data analysis tools
  ☆9Updated 5 years ago
• jaudoux / kamix
  Index and query k-mer matrices in BGZF
  ☆12Updated 7 years ago
• hallamlab / LCAStar
  Alternative taxonomic consensus algorithms based on the NCBI taxonomy tree
  ☆16Updated last year
• edawson / mkmh
  Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.
  ☆24Updated 4 years ago
• lindenb / verticalize
  Simple tool to verticalize text delimited files.
  ☆36Updated last year
• mjsull / HapFlow
  Visualise interstrain recombination from environmental samples.
  ☆26Updated 6 years ago
• shenlab-sinai / region_analysis
  A python script used to annotate genomic intervals.
  ☆18Updated 5 years ago
• roryk / bcbio.rnaseq
  Mostly deprecated in favor of : https://github.com/hbc/bcbioRNASeq. Quality control, differential gene/transcript expression and pathway …
  ☆24Updated 7 years ago
• percyfal / snakemake-rules
  Library of snakemake rules.
  ☆12Updated 6 years ago
• your-highness / normR
  Normalization and difference calling for Next Generation Sequencing (NGS) data via joint multinomial modeling.
  ☆11Updated 3 years ago
• quinlan-lab / vcftidy
  normalize, left-align, trim, validate and clean VCF files
  ☆20Updated 9 years ago
• BenLangmead / qtip
  Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities
  ☆25Updated 5 years ago
• ryanlayer / svv
  Stupid Simple Structural Variant View
  ☆25Updated 8 years ago
• gregorykucherov / mreps
  mreps: software for tandem repeat identification in DNA
  ☆14Updated 5 years ago
• lh3 / lh3-snippets
  ☆14Updated 5 years ago
• brentp / geneimpacts
  prioritize effects of variant annotations from VEP, SnpEff, et al.
  ☆34Updated 6 months ago
• DecodeGenetics / BamHash
  ☆37Updated 4 years ago
• karel-brinda / rnftools
  RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
  ☆14Updated 6 years ago