Repositories list

• GATK-flow

  Public
  Nextflow implementation of the GATK HaplotypeCaller pipeline

  nextflowgatk

  Nextflow

  •2•12•2•1•Updated Dec 2, 2024Dec 2, 2024

• polishCLR

  Public
  A nextflow pipeline for polishing CLR assemblies

  nextflowarrowfreebayes+ 7buscomerqurymerfinbioinformaticspipelinegenomicsassembly

  Nextflow

  •4•16•5•0•Updated Feb 3, 2023Feb 3, 2023

• blast

  Public
  NextFlow implementation of BLAST program

  Nextflow

  •

  MIT License

  •4•3•3•0•Updated Jan 23, 2023Jan 23, 2023

• assemblyStats

  Public
  Run Assembly statistics on a genome assembly (BUSCO and assemblyStats and new_Assemblathon.pl)

  swiftnextflowbusco

  Perl

  •5•4•1•0•Updated Sep 13, 2022Sep 13, 2022

• freebayes

  Public
  Freebayes parallelization using nextflow

  Nextflow

  •0•0•0•0•Updated Aug 1, 2022Aug 1, 2022

• bwamem2

  Public
  Nextflow

  •0•0•0•0•Updated May 4, 2022May 4, 2022

• nanoPolish

  Public
  Polish a nanopore assembly using Racon and Medaka

  nextflowraconmedoka

  Nextflow

  •0•0•0•0•Updated Nov 22, 2021Nov 22, 2021

• nanoQCtrim

  Public
  Performs Nanoplot QC using nanoplot and adaptor trimming using downpore

  Shell

  •0•0•4•0•Updated Oct 20, 2021Oct 20, 2021

• alphafold

  Public
  fast draft, quick testing

  Nextflow

  •0•0•0•0•Updated Aug 19, 2021Aug 19, 2021

• RNAseq

  Public
  RNAseq from fastq reads to gene counts/quantification

  nextflowmultiqcsalmon+ 3kallistogsnapfastqc

  Nextflow

  •0•0•0•0•Updated Aug 13, 2021Aug 13, 2021

• parallel

  Public
  Nextflow

  •0•1•2•0•Updated Feb 11, 2021Feb 11, 2021

• tutorial

  Public
  Tutorial on how to use nextflow to create a workflow for blast

  Nextflow

  •1•3•0•0•Updated Sep 17, 2020Sep 17, 2020