{"repo":"fmalmeida/MpGAP","free":true,"listed":false,"github":"https://github.com/fmalmeida/MpGAP","clone":"git clone https://github.com/fmalmeida/MpGAP.git","description":"Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads","language":"Nextflow","stars":66,"topics":["hybrid-assemblies","illumina","pipeline","genome-assembly","polish","pacbio","nanopore","unicycler","spades","flye"],"license":"GPL-3.0","category":"deployment-docker-iac","readme_excerpt":"MpGAP pipeline A generic multi-platform genome assembly pipeline See the documentation » Report Bug · Request Feature About MpGAP is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. It is an easy to use pipeline that adopts well known software for de novo genome assembly of Illumina, Pacbio and Oxford Nanopore sequencing data through illumina only, long reads only or hybrid modes. This pipeline wraps up the following software: Source :- :- Assemblers Hifiasm, Canu, Flye, Raven, Shasta, wtdbg2, Haslr, Unicycler, Spades, Shovill, Megahit Polishers Nanopolish, Medaka, gcpp, Polypolish and Pilon Quality check Quast, BUSCO and MultiQC Release notes Are you curious about changes between releases? See the changelog. I strongly , vividly , mightily recommend the usage of the latest versions hosted in master branch, which is nextflow's default. + The latest will always have support, bug fixes and generally maitain the same processes (I mainly add things instead of removing) that also were in previous versions. + But, if you really want to execute an earlier release, please see the instructions for that. Versions below 3.0 are no longer supported. Further reading This pipeline has two complementary pipelines (also written in nextflow) for NGS preprocessing and prokaryotic genome annotation that can give the user a comple","default_branch":null,"files":null,"tree":[],"storefront":"/r/fmalmeida","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/fmalmeida/MpGAP/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}