MisoFlow - quadram-institute-bioscience/gmh-sops GitHub Wiki
A pipeline for analysis of bacterial isolates. The initial design, resembling 'Nullabor' from the Torstyverse, was nicknamed NullarFlow.
Usage
nextflow run misoflow.nf --reads 'reads/*_R{1,2}.fastq.gz' --outdir 'misoflow' --assembler unicyler
Description
Analysis of multiple bacterial isolate sequencing reads. Includes: QC, evaluation of contaminants, de novo assembly, gene prediction, detection of AMR and virulence genes and pangenome detection.
Output
The pipeline produces a set of output files and an automatic report.