Alternatives and similar repositories for parabricks-nextflow

Users that are interested in parabricks-nextflow are comparing it to the libraries listed below

• dputhier / pygtftk
  A python package and a set of shell commands to handle GTF files
  ☆48Updated 11 months ago
• genepi / nf-gwas
  A nextflow pipeline to perform state-of-the-art genome-wide association studies.
  ☆67Updated 2 months ago
• nf-core / setup-nextflow
  A GitHub action to install Nextflow
  ☆18Updated this week
• EGA-archive / ont2cram
  Oxford Nanopore HDF/Fast5 to CRAM conversion tool
  ☆22Updated 5 years ago
• goldman-gp-ebi / BOSS-RUNS
  Dynamic, adaptive sampling during nanopore sequencing
  ☆33Updated 3 weeks ago
• nextflow-io / nf-schema
  Functionality for working with pipeline and sample sheet schema files in Nextflow pipelines
  ☆41Updated 3 weeks ago
• vembrane / vembrane
  vembrane filters VCF records using python expressions
  ☆58Updated this week
• COMBINE-lab / oarfish
  long read RNA-seq quantification
  ☆85Updated last month
• bentsherman / nf-boost
  Experimental features for Nextflow
  ☆43Updated 2 months ago
• stjudecloud / workflows
  Bioinformatics workflows developed for and used on the St. Jude Cloud project.
  ☆36Updated this week
• cpockrandt / genmap
  GenMap - Fast and Exact Computation of Genome Mappability
  ☆107Updated 11 months ago
• MultiQC / test-data
  Test data for MultiQC.
  ☆22Updated last week
• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 6 years ago
• snakemake-workflows / dna-seq-varlociraptor
  A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, …
  ☆86Updated this week
• nanoporetech / katuali
  Analysis pipelines from Oxford Nanopore Technologies' Research Division
  ☆50Updated 4 years ago
• Kuanhao-Chao / splam
  ✂️ Deep learning-based splice site predictor that improves spliced alignments
  ☆52Updated 3 months ago
• Midnighter / nextflow-gotchas
  A collection of unexpected challenges and learnings with nextflow and nf-core.
  ☆37Updated last year
• tobiasrausch / vc
  A tutorial on structural variant calling for short read sequencing data
  ☆38Updated 7 months ago
• HKU-BAL / ClairS-TO
  ClairS-TO - a deep-learning method for tumor-only somatic variant calling
  ☆62Updated 2 months ago
• ekg / bamaddrg
  adds sample names and read-group (RG) tags to BAM alignments
  ☆51Updated 4 years ago
• epi2me-labs / pychopper
  cDNA read preprocessing
  ☆71Updated 10 months ago
• Oshlack / STRetch
  Method for detecting STR expansions from short-read sequencing data
  ☆63Updated 3 years ago
• noamteyssier / bedrs
  bedtools-like functionality for interval sets in rust
  ☆52Updated 9 months ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆96Updated last year
• epi2me-labs / wf-alignment
  ☆28Updated 3 weeks ago
• friend1ws / nanomonsv
  SV detection tool for nanopore sequence reads
  ☆91Updated 2 months ago
• fulcrumgenomics / fqtk
  Fast FASTQ sample demultiplexing in Rust.
  ☆62Updated last week
• nf-core / scnanoseq
  Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
  ☆37Updated this week
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆140Updated this week
• tk2 / RetroSeq
  RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…
  ☆66Updated 2 years ago