Alternatives and similar repositories for variantbenchmarking

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

• huangnengCSU / longcallR
  LongcallR is a SNP caller for single molecule long-read RNA-seq data
  ☆72Updated last month
• HKU-BAL / ClairS-TO
  ClairS-TO - a deep-learning method for tumor-only somatic variant calling
  ☆80Updated 2 months ago
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆58Updated last year
• fakedrtom / SVAFotate
  ☆44Updated last year
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆82Updated 11 months ago
• TrinityCTAT / CTAT-LR-fusion
  fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector
  ☆24Updated this week
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆64Updated last year
• vicsanga / Postre
  POSTRE: Prediction Of STRuctural variant Effects
  ☆28Updated last month
• bioinfo-chru-strasbourg / vcf2circos
  python plotly Circos from VCF
  ☆40Updated last year
• SciLifeLab / TIDDIT
  TIDDIT - structural variant calling
  ☆78Updated 2 months ago
• genomic-medicine-sweden / nallo
  An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.
  ☆42Updated this week
• nf-core / isoseq
  Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed …
  ☆49Updated 2 months ago
• nf-core / rnavar
  gatk4 RNA variant calling pipeline
  ☆59Updated 2 weeks ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆65Updated 3 weeks ago
• ygidtu / trackplot
  trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and fu…
  ☆99Updated 2 months ago
• cortes-ciriano-lab / savana
  Somatic structural variant caller for long-read data
  ☆87Updated 2 months ago
• nspies / svviz2
  for visual evaluation of read support for structural variation
  ☆56Updated last year
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆63Updated 8 months ago
• srbehera / DRAGEN_Analysis
  ☆38Updated last year
• fritzsedlazeck / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆48Updated 5 years ago
• vembrane / vembrane
  vembrane filters VCF records using python expressions
  ☆68Updated last month
• epi2me-labs / modbam2bed
  ☆52Updated 4 months ago
• fulcrumgenomics / fqtk
  Fast FASTQ sample demultiplexing in Rust.
  ☆66Updated last week
• hms-dbmi / chromoscope
  Interactive multiscale visualization for structural variation in human genomes
  ☆71Updated last week
• nanoporegenomics / napu_wf
  WDL workflows for variant calling and assembly using ONT
  ☆38Updated this week
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆50Updated 5 years ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆57Updated last week
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆38Updated 10 months ago
• nf-core / vscode-extensionpack
  A VSCode extension pack for nf-core developers.
  ☆15Updated 11 months ago
• COMBINE-lab / oarfish
  long read RNA-seq quantification
  ☆103Updated this week