MpGAP¶

MpGAP is a pipeline developed with Nextflow and Docker. It was designed to provide an easy-to-use framework for de novo genome assembly of Illumina, Pacbio and Oxford Nanopore sequencing data through illumina only, long reads only or hybrid modes.

It wraps up the following tools:

Analysis steps	Used software
Long reads assembly	Canu, Flye, Unicycler, Raven, Shasta and wtdbg2
Hybrid assembly	Haslr, Unicycler and SPAdes
Short reads assembly	Shovill, Unicycler, Megahit and SPAdes
Assembly polishing	Nanopolish, Medaka, gcpp and Pilon
Assembly QC	Quast and MultiQC

Support Contact¶

Whenever a doubt arise feel free to contact me at almeidafmarques@gmail.com