Alternatives and similar repositories for ensembl-vep:

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

• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆366Updated 3 years ago
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆432Updated last week
• pcingola / SnpEff
  ☆265Updated last month
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆460Updated 3 weeks ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆540Updated 8 months ago
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆240Updated this week
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆414Updated 2 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆597Updated 10 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆423Updated this week
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆744Updated 7 months ago
• Illumina / manta
  Structural variant and indel caller for mapped sequencing data
  ☆422Updated 2 years ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆498Updated last year
• ucscGenomeBrowser / kent
  UCSC Genome Browser source tree. Stable branch: "beta".
  ☆233Updated this week
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆400Updated 2 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆314Updated 3 years ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆491Updated 2 weeks ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆381Updated 3 months ago
• Gaius-Augustus / BRAKER
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…
  ☆392Updated 2 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆431Updated last year
• STAR-Fusion / STAR-Fusion
  STAR-Fusion codebase
  ☆239Updated last month
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆311Updated 9 months ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆797Updated 8 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆489Updated last year
• nanoporetech / medaka
  Sequence correction provided by ONT Research
  ☆443Updated 5 months ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆496Updated this week
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆355Updated 3 months ago
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆588Updated last week
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆330Updated this week
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆583Updated 2 weeks ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆817Updated 6 months ago