nf-core / variantbenchmarking

Related projects ⓘ

Alternatives and complementary repositories for variantbenchmarking

• genomic-medicine-sweden / nallo
  An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.
  ☆19Updated this week
• epi2me-labs / wf-basecalling
  ☆33Updated 2 weeks ago
• nf-core / detaxizer
  A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…
  ☆14Updated this week
• nextflow-io / nf-co2footprint
  [WIP] A Nextflow plugin to estimate the CO2 footprint of pipeline runs.
  ☆14Updated last month
• nf-core / multiplesequencealign
  A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.
  ☆22Updated 2 weeks ago
• nextflow-io / nf-validation
  Params validation plugin for Nextflow pipelines
  ☆48Updated 3 months ago
• lh3 / minipileup
  Simple pileup-based variant caller
  ☆81Updated 7 months ago
• fakedrtom / SVAFotate
  ☆39Updated last month
• ryanlayer / stix
  Structural Variant Index
  ☆69Updated last week
• epi2me-labs / modbam2bed
  ☆47Updated 2 months ago
• mribeirodantas / NextflowSnippets
  This repository hosts a large collection of Nextflow snippets
  ☆57Updated 5 months ago
• Illumina / witty.er
  What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
  ☆29Updated last year
• sirselim / guppy_parameter_optimiser
  A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
  ☆31Updated 2 years ago
• cortes-ciriano-lab / savana
  Somatic structural variant caller for long-read data
  ☆47Updated this week
• snakemake-workflows / dna-seq-benchmark
  A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
  ☆12Updated this week
• Maggi-Chen / DeBreak
  Structural variant caller for real-time long-read sequencing data
  ☆55Updated 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
  ☆38Updated last year
• monarch-initiative / SvAnna
  Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing
  ☆33Updated 4 months ago
• vembrane / vembrane
  vembrane filters VCF records using python expressions
  ☆57Updated last month
• kensung-lab / INSurVeyor
  An insertion caller for Illumina paired-end WGS data.
  ☆22Updated 3 months ago
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆53Updated 3 weeks ago
• GeneDx / scramble
  ☆36Updated 6 months ago
• daewoooo / SVbyEye
  ☆69Updated last month
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆56Updated 3 weeks ago
• bentsherman / nf-boost
  Experimental features for Nextflow
  ☆31Updated last month
• bcgsc / straglr
  Tandem repeat expansion detection or genotyping from long-read alignments
  ☆67Updated last month
• kjenike / panagram
  ☆57Updated 3 weeks ago
• rrwick / MinION-desktop
  Scripts and programs for the Holt Lab's MinION desktop
  ☆32Updated 3 years ago
• PacificBiosciences / jasmine
  Predict 5mC in PacBio HiFi reads
  ☆32Updated last week
• kcleal / dysgu
  Toolkit for calling structural variants using short or long reads
  ☆95Updated 2 weeks ago