Alternatives and similar repositories for snakemake-workflows

Users that are interested in snakemake-workflows are comparing it to the libraries listed below

• najoshi / sabre
  ☆63Updated 5 years ago
• MVesuviusC / primerTree
  PrimerTree: Visually Assessing the Specificity and Informativeness of Primer Pairs
  ☆52Updated 2 months ago
• jdidion / atropos
  An NGS read trimming tool that is specific, sensitive, and speedy. (production)
  ☆126Updated 8 months ago
• ssadedin / bazam
  A read extraction and realignment tool for next generation sequencing data
  ☆104Updated 3 years ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆76Updated 3 years ago
• peterjc / picobio
  Miscellaneous Bioinformatics scripts etc mostly in Python
  ☆45Updated 2 weeks ago
• grenaud / deML
  Maximum likelihood demultiplexing
  ☆50Updated 11 months ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• lh3 / tabtk
  Toolkit for processing TAB-delimited format
  ☆62Updated last year
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 7 years ago
• frankMusacchia / Annocript
  Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved …
  ☆56Updated 5 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated 2 years ago
• IARCbioinfo / IARC-nf
  List of IARC bioinformatics pipelines and resources
  ☆56Updated last month
• wdecoster / nano-snakemake
  A snakemake pipeline for SV analysis from nanopore genome sequencing
  ☆52Updated 5 years ago
• mw55309 / Kraken_db_install_scripts
  Updated Kraken DB install scripts to cope with new-ish NCBI structure
  ☆48Updated 8 years ago
• SciLifeLab / NGI-RNAseq
  Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
  ☆51Updated 7 years ago
• mritchielab / long_read_tools
  A catalogue of available long read sequencing data analysis tools
  ☆83Updated 2 weeks ago
• Trinotate / Trinotate.github.io
  web documentation for Trinotate
  ☆48Updated 2 years ago
• fbreitwieser / bamcov
  Quickly calculate and visualize sequence coverage in alignment files
  ☆101Updated 6 years ago
• lh3 / bfc
  High-performance error correction for Illumina resequencing data
  ☆74Updated 9 years ago
• merenlab / illumina-utils
  A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
  ☆94Updated last month
• ngsutils / ngsutils
  Tools for next-generation sequencing analysis
  ☆89Updated 6 years ago
• gatk-workflows / broad-prod-wgs-germline-snps-indels
  Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…
  ☆57Updated 5 years ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆143Updated 4 months ago
• alastair-droop / fqtools
  An efficient FASTQ manipulation suite
  ☆138Updated 5 years ago
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 6 years ago
• lpryszcz / bin
  My bioinfo toolbox
  ☆50Updated 11 months ago
• vsbuffalo / scythe
  A 3'-end adapter contaminant trimmer
  ☆95Updated 7 years ago
• Oshlack / Lace
  Building SuperTranscripts: A linear representation of transcriptome data
  ☆68Updated 4 years ago