Alternatives and similar repositories for NGS-pipe

Users that are interested in NGS-pipe are comparing it to the libraries listed below

• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆93Updated 10 months ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆140Updated 3 weeks ago
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆136Updated 2 years ago
• ewels / AWS-iGenomes
  Documentation and description of AWS iGenomes S3 resource.
  ☆116Updated 9 months ago
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆131Updated last year
• davetang / learning_vcf_file
  Learning the Variant Call Format
  ☆144Updated last month
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆142Updated 2 years ago
• aryeelab / guideseq
  Analysis pipeline for the GUIDE-seq assay.
  ☆80Updated 2 years ago
• crazyhottommy / pyflow-ChIPseq
  a snakemake pipeline to process ChIP-seq files from GEO or in-house
  ☆110Updated 5 years ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 4 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆147Updated last week
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆117Updated 7 months ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆38Updated 4 years ago
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆119Updated 7 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆170Updated last year
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆172Updated last year
• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆92Updated 3 months ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆77Updated 5 years ago
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆158Updated 3 weeks ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• kundajelab / chipseq_pipeline
  AQUAS TF and histone ChIP-seq pipeline
  ☆110Updated 3 years ago
• mskcc / facets
  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
  ☆151Updated 2 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆138Updated 5 years ago
• guigolab / ggsashimi
  Command-line tool for the visualization of splicing events across multiple samples
  ☆130Updated last year
• maasha / biopieces
  Biopieces is a bioinformatic framework of tools easily used and easily created.
  ☆142Updated 7 years ago
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆224Updated last year
• h3abionet / h3agwas
  GWAS Pipeline for H3Africa
  ☆111Updated 3 months ago
• gagneurlab / drop
  Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
  ☆154Updated 3 weeks ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago