Alternatives and similar repositories for ref-gen

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

• huangnengCSU / longcallR
  LongcallR is a SNP caller for single molecule long-read RNA-seq data
  ☆66Updated this week
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 11 months ago
• rrazaghi / modbamtools
  Set of tools to manipulate and visualize modified base bam files
  ☆56Updated 3 years ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆63Updated 11 months ago
• adamewing / tldr
  Identify and annotate TE-mediated insertions in long-read sequence data
  ☆42Updated 2 months ago
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 5 years ago
• fakedrtom / SVAFotate
  ☆44Updated last year
• fiberseq / FIRE
  A Snakemake workflow for calling Fiber-seq Inferred Regulatory Elements (FIREs) on single molecules.
  ☆25Updated 2 months ago
• ksahlin / ultra
  Long-read splice alignment with high accuracy
  ☆63Updated 11 months ago
• fritzsedlazeck / Spectre
  Copy number caller for long read data including SNV utilization
  ☆67Updated 5 months ago
• treangenlab / methphaser
  MethPhaser: methylation-based haplotype phasing of human genomes
  ☆49Updated 6 months ago
• fritzsedlazeck / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆48Updated 5 years ago
• ksahlin / isONcorrect
  Error correction of ONT transcript reads
  ☆58Updated 2 years ago
• TrinityCTAT / CTAT-LR-fusion
  fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector
  ☆22Updated this week
• LappalainenLab / lorals
  ☆36Updated 2 years ago
• zd1 / telseq
  A software for calculating telomere length
  ☆71Updated 6 years ago
• cortes-ciriano-lab / savana
  Somatic structural variant caller for long-read data
  ☆80Updated 3 months ago
• evotools / nf-LO
  A Nextflow workflow to generate lift over files for any pair of genomes
  ☆68Updated 3 months ago
• WGLab / LongReadSum
  ☆24Updated last week
• PacificBiosciences / sv-benchmark
  Public Benchmark of Long-Read Structural Variant Caller on PacBio CCS HG002 Data
  ☆51Updated 4 years ago
• SciLifeLab / TIDDIT
  TIDDIT - structural variant calling
  ☆76Updated 5 months ago
• KolmogorovLab / minda
  ☆23Updated 5 months ago
• vahidAK / NanoMethPhase
  Methylation Phasing for Nanopore Sequencing
  ☆48Updated 2 years ago
• josiegleeson / BamSlam
  Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files
  ☆14Updated last year
• kcleal / dysgu
  Toolkit for calling structural variants using short or long reads
  ☆109Updated last week
• bioinfo-chru-strasbourg / vcf2circos
  python plotly Circos from VCF
  ☆39Updated last year
• PacificBiosciences / sawfish
  Joint structural variant and copy number variant caller for HiFi sequencing data
  ☆60Updated this week
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆50Updated 2 years ago
• PacificBiosciences / pb-human-wgs-workflow-snakemake
  DEPRECATED - Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads
  ☆39Updated last year
• MeHelmy / princess
  ☆81Updated 6 months ago