Alternatives and similar repositories for VEP_plugins:

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

• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆156Updated last year
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆211Updated 7 months ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆157Updated 5 months ago
• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆79Updated 2 weeks ago
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆178Updated this week
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆206Updated this week
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆99Updated 3 months ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆115Updated last month
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆140Updated last year
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆144Updated last year
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆111Updated 7 months ago
• ncbi / TPMCalculator
  TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
  ☆128Updated 7 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆235Updated last month
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆140Updated 2 years ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆150Updated 2 years ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆128Updated 7 months ago
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆120Updated 2 years ago
• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆82Updated last week
• AstraZeneca-NGS / VarDict
  VarDict
  ☆192Updated last year
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆132Updated 3 weeks ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆232Updated 3 months ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆142Updated 5 months ago
• nf-core / raredisease
  Call and score variants from WGS/WES of rare disease patients.
  ☆94Updated this week
• Illumina / ExpansionHunterDenovo
  A suite of tools for detecting expansions of short tandem repeats
  ☆80Updated last year
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 3 years ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆218Updated last year
• VanLoo-lab / ascat
  ASCAT R package
  ☆174Updated 2 months ago
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆123Updated 4 years ago