Alternatives and similar repositories for ensembl-vep

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

• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆425Updated 2 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆444Updated last year
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆457Updated this week
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆449Updated 3 weeks ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆475Updated 2 weeks ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆437Updated last year
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆375Updated 3 years ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆723Updated last week
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆764Updated 2 weeks ago
• Illumina / manta
  Structural variant and indel caller for mapped sequencing data
  ☆434Updated 2 years ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆422Updated 6 months ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆513Updated 4 months ago
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆515Updated this week
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆503Updated 8 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆389Updated 7 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆517Updated last year
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆242Updated last week
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆320Updated last month
• pcingola / SnpEff
  ☆279Updated 5 months ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆504Updated 3 weeks ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆477Updated 4 months ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆985Updated 4 months ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆826Updated last year
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆379Updated 2 weeks ago
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆374Updated last month
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆319Updated 3 years ago
• nanopore-wgs-consortium / NA12878
  Data and analysis for NA12878 genome on nanopore
  ☆392Updated 2 years ago
• vcftools / vcftools
  A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
  ☆534Updated 2 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆748Updated 3 months ago