Alternatives and similar repositories for ref-gen

Users that are interested in ref-gen are comparing it to the libraries listed below

• fakedrtom / SVAFotate
  ☆44Updated last year
• rrazaghi / modbamtools
  Set of tools to manipulate and visualize modified base bam files
  ☆59Updated 3 years ago
• huangnengCSU / longcallR
  LongcallR is a SNP caller for single molecule long-read RNA-seq data
  ☆72Updated last month
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆58Updated last year
• ksahlin / isONcorrect
  Error correction of ONT transcript reads
  ☆58Updated 2 years ago
• fritzsedlazeck / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆48Updated 5 years ago
• SciLifeLab / TIDDIT
  TIDDIT - structural variant calling
  ☆78Updated 2 months ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆64Updated last year
• DavidsonGroup / flexiplex
  The Flexible Demultiplexer
  ☆39Updated last month
• ksahlin / ultra
  Long-read splice alignment with high accuracy
  ☆64Updated last year
• cortes-ciriano-lab / savana
  Somatic structural variant caller for long-read data
  ☆87Updated 2 months ago
• treangenlab / methphaser
  MethPhaser: methylation-based haplotype phasing of human genomes
  ☆52Updated 11 months ago
• bioinfo-chru-strasbourg / vcf2circos
  python plotly Circos from VCF
  ☆40Updated last year
• PacificBiosciences / pb-human-wgs-workflow-snakemake
  DEPRECATED - Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads
  ☆39Updated 2 years ago
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 5 years ago
• kcleal / dysgu
  Toolkit for calling structural variants using short or long reads
  ☆115Updated last week
• genomic-medicine-sweden / nallo
  An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.
  ☆42Updated this week
• fritzsedlazeck / Spectre
  Copy number caller for long read data including SNV utilization
  ☆68Updated 10 months ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆143Updated 5 months ago
• adamewing / tldr
  Identify and annotate TE-mediated insertions in long-read sequence data
  ☆46Updated 7 months ago
• TimD1 / vcfdist
  vcfdist: Accurately benchmarking phased variant calls
  ☆84Updated 4 months ago
• lh3 / minipileup
  Simple pileup-based variant caller
  ☆95Updated 9 months ago
• WGLab / LongReadSum
  ☆27Updated 4 months ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆102Updated last year
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆121Updated 4 months ago
• epi2me-labs / modbam2bed
  ☆52Updated 4 months ago
• BimberLab / DISCVRSeq
  A collection of command line tools for working with sequencing data
  ☆52Updated last week
• MeHelmy / princess
  ☆84Updated 11 months ago
• DecodeGenetics / svimmer
  Structural variant merging tool
  ☆57Updated last year
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆82Updated 11 months ago