Alternatives and similar repositories for ensembl-pipeline:

Users that are interested in ensembl-pipeline are comparing it to the libraries listed below

• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆119Updated 2 years ago
• YangLab / CIRCexplorer
  A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, …
  ☆60Updated 5 years ago
• ExpressionAnalysis / ea-utils
  Automatically exported from code.google.com/p/ea-utils
  ☆95Updated last year
• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆77Updated last week
• YangLab / CIRCexplorer2
  circular RNA analysis toolset
  ☆80Updated 4 months ago
• 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  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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…
  ☆76Updated 4 years ago
• Tong-Chen / NGS
  Scripts for next generation sequencing
  ☆48Updated 5 years ago
• likelet / LncPipe
  A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets
  ☆83Updated 2 years ago
• Kennedy-Lab-UW / Duplex-Sequencing
  ☆57Updated 4 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆191Updated last year
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆154Updated 4 months ago
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆141Updated 4 months ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆121Updated 4 years ago
• MathOnco / NeoPredPipe
  Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
  ☆110Updated 4 months ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆103Updated 3 years ago
• andyrimmer / Platypus
  Platypus Variant Caller
  ☆105Updated 6 months ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆126Updated 6 months ago
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆118Updated 6 years ago
• mgonzalezporta / TeachingMaterial
  RNA-seq data analysis practical
  ☆60Updated 10 years ago
• tseemann / PEAR
  Pair-End AssembeR
  ☆29Updated 10 years ago
• StanfordBioinformatics / SJM
  Simple Job Manager
  ☆58Updated 7 years ago
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆124Updated 4 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆155Updated last year
• ncbi / TPMCalculator
  TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
  ☆126Updated 6 months ago
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆143Updated this week
• cbg-ethz / NGS-pipe
  NGS-pipe: next-generation sequencing pipelines for precision oncology
  ☆109Updated 5 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆96Updated 2 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆208Updated 6 months ago