Alternatives and similar repositories for patterns

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

• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆396Updated last week
• nextflow-io / awesome-nextflow
  A curated list of nextflow based pipelines
  ☆619Updated 6 months ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆351Updated last month
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆515Updated last month
• GoekeLab / bioinformatics-workflows
  minimal example implementations for bioinformatics workflow managers
  ☆280Updated 4 years ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆451Updated last year
• fulcrumgenomics / fgbio
  Tools for working with genomic and high throughput sequencing data.
  ☆350Updated last week
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆348Updated last month
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆493Updated last week
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆398Updated 2 months ago
• nextflow-io / training
  Nextflow training material
  ☆209Updated this week
• nf-core / tools
  Python package with helper tools for the nf-core community.
  ☆285Updated last week
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆262Updated 2 years ago
• assemblerflow / flowcraft
  FlowCraft: a component-based pipeline composer for omics analysis using Nextflow.
  ☆246Updated 5 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆279Updated 2 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆258Updated 3 months ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆302Updated 2 years ago
• pachterlab / sleuth
  Differential analysis of RNA-Seq
  ☆312Updated 7 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆557Updated last year
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆440Updated 5 months ago
• snakemake / snakemake-wrappers
  This is the development home of the Snakemake wrapper repository, see
  ☆238Updated last week
• pcingola / SnpEff
  ☆299Updated last month
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆322Updated 3 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆357Updated 8 months ago
• broadinstitute / warp
  Warp Analysis Research Pipelines
  ☆224Updated this week
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆479Updated 3 weeks ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
  ☆185Updated last week
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆752Updated 5 months ago
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆392Updated 4 months ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆218Updated last month