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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

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