medusa2's Introduction

MeDuSa2

From https://github.com/combogenomics/medusa A draft genome scaffolder that uses multiple reference genomes in a graph-based approach. Thanks to EBosi and gianlucacolotto.

Requirements:

Mummer (sudo apt-get install mummer)
Minimap2 (sudo apt-get install minimap2)
Python > 3.6
Python modules: networkx, biopython, flask

medusa2web: contains medusa2web and script for running medusa2. Replace with your path on launcher.sh and start python3 medusa2web.py (http://127.0.0.1:5000/)

medusa2standalone: contains medusa2 standalone version for running directly from bash

Run & Required parameters: python3 medusa.py -i input_filename -f reference_folder

Optional parameters:

                  -s skipmap_folder (folder that contains coords or paf file generated previously from mummer or minimap2, with these you can skip alignment step)

                  -a use Minimap2 aligner instead of Mummer aligner
                  
                  -t <n> number of processes used for alignment step
                  
                  -v <n> verbosity level
                  
                  -o output folder for support files and scaffold writing

Under folder /medusa2standalone/BenchmarkMedusa2/ you can see many usage example for running the tool! In dataset_medusa.txt you have a link for dataset used about BCEN,ECOL,MTUB,RSPH,SAUR,THAL,CELEGANS.

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