Alternatives and similar repositories for bioinformatics-workflows

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

• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated this week
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆275Updated 11 months ago
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆210Updated last week
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆252Updated 4 months ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆331Updated 2 months ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆341Updated 10 months ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆211Updated last month
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆226Updated this week
• nextflow-io / training
  Nextflow training material
  ☆171Updated this week
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆217Updated 2 months ago
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆102Updated 6 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆543Updated 10 months ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆224Updated 3 weeks ago
• CompEpigen / figeno
  Tool for plotting sequencing data along genomic coordinates.
  ☆294Updated 2 weeks ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆167Updated this week
• al2na / methylKit
  R package for DNA methylation analysis
  ☆231Updated 3 months ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆166Updated this week
• nf-core / fetchngs
  Pipeline to fetch metadata and raw FastQ files from public databases
  ☆175Updated this week
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆329Updated 3 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆214Updated last month
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆254Updated last year
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 3 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆241Updated 2 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆268Updated last year
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆309Updated 4 years ago
• griffithlab / rnabio.org
  website for the rnaseq course
  ☆101Updated 2 weeks ago
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆201Updated last week
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆299Updated last year
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆416Updated 5 months ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆124Updated 2 years ago