Alternatives and similar repositories for variantbenchmarking

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

• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 10 months ago
• HKU-BAL / ClairS-TO
  ClairS-TO - a deep-learning method for tumor-only somatic variant calling
  ☆66Updated 5 months ago
• fakedrtom / SVAFotate
  ☆44Updated 11 months ago
• nf-core / oncoanalyser
  A comprehensive cancer DNA/RNA analysis and reporting pipeline
  ☆80Updated this week
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆62Updated 10 months ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 6 months ago
• SciLifeLab / TIDDIT
  TIDDIT - structural variant calling
  ☆76Updated 4 months ago
• fulcrumgenomics / fqtk
  Fast FASTQ sample demultiplexing in Rust.
  ☆64Updated 3 months ago
• nf-core / rnavar
  gatk4 RNA variant calling pipeline
  ☆52Updated this week
• huangnengCSU / longcallR
  LongcallR is a SNP caller for single molecule long-read RNA-seq data
  ☆63Updated 2 weeks ago
• 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 …
  ☆45Updated last month
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆63Updated 3 months ago
• Kuanhao-Chao / splam
  ✂️ Deep learning-based splice site predictor that improves spliced alignments
  ☆54Updated 6 months ago
• zavolanlab / zarp
  The Zavolab Automated RNA-seq Pipeline
  ☆35Updated last month
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆50Updated 5 years ago
• srbehera / DRAGEN_Analysis
  ☆34Updated last year
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆49Updated this week
• deepomicslab / SpecHLA
  SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …
  ☆49Updated last week
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆38Updated 5 months ago
• genomic-medicine-sweden / nallo
  An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.
  ☆34Updated this week
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆60Updated 2 months ago
• TrinityCTAT / CTAT-LR-fusion
  fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector
  ☆22Updated 3 weeks ago
• hms-dbmi / chromoscope
  Interactive multiscale visualization for structural variation in human genomes
  ☆70Updated 3 weeks ago
• nf-core / vscode-extensionpack
  A VSCode extension pack for nf-core developers.
  ☆15Updated 5 months ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆97Updated last year
• lh3 / ref-gen
  Human reference genome analysis sets
  ☆53Updated 2 years ago
• nextflow-io / nf-validation
  Params validation plugin for Nextflow pipelines
  ☆48Updated last year
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆50Updated 2 years ago
• ulelab / ultraplex
  Ultra-fast 5' and 3' demultiplexer
  ☆28Updated last year
• fritzsedlazeck / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆48Updated 5 years ago