Alternatives and similar repositories for awesome-nextflow

Users that are interested in awesome-nextflow are comparing it to the libraries listed below

• nextflow-io / patterns
  A curated collection of Nextflow implementation patterns
  ☆365Updated last year
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆741Updated 3 months ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆510Updated 2 weeks ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated last week
• BioContainers / containers
  Bioinformatics containers
  ☆757Updated last month
• jdidion / biotools
  A list of useful bioinformatics resources
  ☆616Updated 6 months ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆845Updated last year
• crazyhottommy / bioinformatics-one-liners
  Bioinformatics one liners from Ming Tang
  ☆495Updated 5 years ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,372Updated last week
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆703Updated 6 months ago
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆492Updated last week
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆514Updated last month
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆544Updated last month
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆841Updated last year
• pachterlab / ffq
  A tool to find sequencing data and metadata from public databases.
  ☆591Updated last year
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆509Updated last week
• nf-core / tools
  Python package with helper tools for the nf-core community.
  ☆275Updated this week
• mdshw5 / pyfaidx
  Efficient pythonic random access to fasta subsequences
  ☆479Updated last month
• jorvis / biocode
  Bioinformatics code libraries and scripts
  ☆546Updated 3 months ago
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,118Updated 2 weeks ago
• cmdcolin / awesome-genome-visualization
  A list of interesting genome browser and genome visualization programs
  ☆1,014Updated 2 weeks ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆434Updated 2 months ago
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆528Updated 3 months ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆346Updated last month
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆489Updated last month
• chapmanb / bcbb
  Incubator for useful bioinformatics code, primarily in Python and R
  ☆632Updated 8 months ago
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆849Updated 4 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆758Updated last week
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆454Updated last year
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,503Updated 4 months ago