digenoma lab

.github

bam2cram

A repository to convert BAM->CRAM files

mag

Assembly and binning of metagenomes

alignment-nf

Whole Exome/Whole Genome Sequencing alignment pipeline

alnsl

Nextflow pipeline for short-read alignment

call_snv

A nextflow pipeline to call SNV from short-read sequences

fastqc-nf

hic-scaffolding-nf

Nextflow pipeline for scaffolding genome assemblies with Hi-C reads

k-count-nf

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

longreadstats

mutect-nf

Mutect pipeline with Nextflow

nextflow

A DSL for data-driven computational pipelines

nf-ngscheckmate

Nextflow workflow running NGScheckmate

prok-annotate

Annotation pipeline for prokaryotic genomes

purple-nf

Nextflow pipeline for CNV calling with PURPLE

somatic_point_mutations

call somatic point mutations from tumor/normal pairs

strelka2-nf

viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

wengan_demo

This repository contains a test dataset and the instructions to run Wengan (version 0.1).

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.

Germline-StructuralV-nf

Germline structural variant calling pipeline for short read WGS datasets

HBW

Hybrid Binning Wengan (HBW)

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-mag-depths

A nextflow pipeline to calculate depth of coverage from a metagenomic set of bins

oncovirus

prediction of somatic virus integration from WGS using hmftools

ppilon

Nextflow pipeline for polising a large genome using pilon

spg

Simple Pan-Genome workflow for MAGs