Alternatives and similar repositories for NGS-pipe:

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

• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆157Updated 5 months ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 3 months ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆111Updated 7 months ago
• davetang / learning_vcf_file
  Learning the Variant Call Format
  ☆138Updated 10 months ago
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆119Updated 6 years ago
• Zhong-Lab-UCSD / Genomic-Interactive-Visualization-Engine
  Genomic Interactive Visualization Engine
  ☆145Updated 2 years ago
• likelet / LncPipe
  A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets
  ☆82Updated 2 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆96Updated 3 years ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆38Updated 3 years ago
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆132Updated 2 years ago
• SciLifeLab / NGI-RNAseq
  Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
  ☆51Updated 6 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆128Updated 7 months ago
• ncbi / TPMCalculator
  TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
  ☆128Updated 7 months ago
• VanLoo-lab / ascat
  ASCAT R package
  ☆174Updated 2 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆156Updated last year
• ewels / AWS-iGenomes
  Documentation and description of AWS iGenomes S3 resource.
  ☆109Updated 2 months ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆132Updated 3 weeks ago
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆147Updated 5 months ago
• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆79Updated 2 weeks ago
• Czh3 / NGSTools
  Next-Generation Sequencing(NGS) toolkits.
  ☆45Updated 8 years ago
• mskcc / facets
  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
  ☆148Updated last year
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆140Updated 2 years ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆100Updated 9 months ago
• ding-lab / CharGer
  Characterization of Germline variants
  ☆98Updated 2 years ago
• SciLifeLab / Sarek
  Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
  ☆133Updated 5 years ago
• raerose01 / deconstructSigs
  deconstructSigs
  ☆140Updated last year
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆122Updated 4 years ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 3 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆144Updated last year
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆212Updated 8 months ago