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alignment-nf

Whole Exome/Whole Genome Sequencing alignment pipeline

alnsl

Nextflow pipeline for short-read alignment

ampliconarchitect-nf

Nextflow pipeline to discover ecDNA on cancer genomes

assemblystats

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

bacannot

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

bam2cram

A repository to convert BAM->CRAM files

call_snv

A nextflow pipeline to call SNV from short-read sequences

discovarexp-51885

Not my work, just a repo for DiscovarDenovo version 51885

fast-sg

Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.

fastmin-sg

FAST-SG idea implemented using minimizer and chaining with the minimap2 API.

fastqc-nf

germline-structuralv-nf

Germline structural variant calling pipeline for short read WGS datasets

hbw

Hybrid Binning Wengan (HBW)

hic-scaffolding-nf

Nextflow pipeline for scaffolding genome assemblies with Hi-C reads

intervalmiss

Ultra-fast detection and split of miss-assembled contigs using pair-end reads.

k-count-nf

A nextflow pipeline to count k-mers and estimate genome size from WGS data

liger

Synthetic Scaffolding Graph construction, Overlaps, Scaffolding, Validation, Gap filling and Polishing

longreadstats

mag

Assembly and binning of metagenomes

mutect-nf

Mutect pipeline with Nextflow

mutsig

Mutational signature analysis of WGS data

nextflow

A DSL for data-driven computational pipelines

nf-bakta

A Nextflow pipeline for the annotation of bacterial genomes or MAGs running Bakta

nf-gene-fusions

A nextflow pipeline to call somatic gene fusions

nf-groot

A Nextflow pipeline for running Groot: a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples.

nf-hla-neo

Pipeline to make neonantigen prediction from WGS data

nf-mag-depths

nf-ngscheckmate

Nextflow workflow running NGScheckmate

oncovirus

prediction of somatic virus integration from WGS using hmftools