Welcome to MpGAP pipeline documentation
About
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.
Workflow
The pipeline wraps up the following tools and analyses:
Software | Analysis |
---|---|
Hifiasm, Canu, Flye, Unicycler, Raven, Shasta and wtdbg2 | Long reads assembly |
Haslr, Unicycler and SPAdes | Hybrid assembly |
Shovill, Unicycler, Megahit and SPAdes | Short reads assembly |
Nanopolish, Medaka, gcpp, Polypolish and Pilon | Assembly polishing |
Quast, BUSCO and MultiQC | Assembly QC |
Quickstart
A quickstart is available so you can quickly get the gist of the pipeline's capabilities.
Usage
The pipeline's common usage is very simple as shown below:
# usual command-line
nextflow run fmalmeida/mpgap \
-profile docker \
--output ./results \
--tracedir ./results/pipeline_info \
--input input.yml \
--max_cpus 20 \
--max_memory '40.GB' \
...
Quote
Some parameters are required, some are not. Please read the pipeline's manual reference to understand each parameter.
Citation
In order to cite this pipeline, please refer to:
Almeida FMd, Campos TAd and Pappas Jr GJ. Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation. F1000Research 2023, 12:1205 (https://doi.org/10.12688/f1000research.139488.1)
Support contact
Whenever a doubt arise feel free to contact me via the github issues.