Alternatives and similar repositories for tools

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

• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆395Updated last week
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆395Updated last month
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆278Updated 2 years ago
• GoekeLab / bioinformatics-workflows
  minimal example implementations for bioinformatics workflow managers
  ☆281Updated 4 years ago
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆310Updated last year
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆228Updated last month
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆262Updated 2 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆351Updated last week
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆557Updated last year
• vanheeringen-lab / genomepy
  genes and genomes at your fingertips
  ☆406Updated 2 months ago
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆393Updated 3 weeks ago
• nextflow-io / training
  Nextflow training material
  ☆207Updated this week
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆348Updated 2 weeks ago
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆550Updated last week
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆279Updated 7 months ago
• nextflow-io / patterns
  A curated collection of Nextflow implementation patterns
  ☆367Updated 2 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆257Updated 3 months ago
• assemblerflow / flowcraft
  FlowCraft: a component-based pipeline composer for omics analysis using Nextflow.
  ☆245Updated 4 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆276Updated 2 months ago
• nf-core / fetchngs
  Pipeline to fetch metadata and raw FastQ files from public databases
  ☆184Updated last month
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆290Updated last month
• nf-core / rnafusion
  RNA-seq analysis pipeline for detection of gene-fusions
  ☆169Updated last week
• snakemake / snakemake-wrappers
  This is the development home of the Snakemake wrapper repository, see
  ☆238Updated this week
• broadinstitute / viral-ngs
  [THIS REPO IS DEPRECATED] see newer repos: https://github.com/broadinstitute/viral-core https://github.com/broadinstitute/viral-assemble …
  ☆195Updated last year
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆301Updated 2 years ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆217Updated 2 weeks ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆250Updated 3 weeks ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆300Updated 2 months ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆329Updated 7 months ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆273Updated last month