Nimauric / Mapler

A metagenome assembly and evaluation pipeline, focused on hi-fi long reads, but with support for lo-fi long reads and hybrid assemblies

Mapler (MAEPLR)

Metagenome Assembly and Evaluation Pipeline for Long Reads

Description

The aim of this repository is to compare long-reads metagenomic assemblers, focusing on hi-fi assemblers, but with support for lo-fi long reads assemblers and hybrid assemblers.

This pipeline was used to study assembly of complex ecosystems and their evaluation, the results of which can be found here : https://inria.hal.science/hal-04142837

Installation

Clone the repository in a cluster with slurm and conda support, then run source initialise_env.sh

Usage

Edit the config.yamlfile to specify the name and path of runs of reads you wish to assemble, and comment or uncomment assemblers and metrics you wish to use. If you use reference-based metrics, you must specify the path to a folder (reference-genomes) containing reference genomes, and a csv file (abundance-information) containing, for each reference genome, their group (I advice grouping them by abundance)

Then run source activate_env.sh and, if you want to previsualise the pipeline, ./np_pipeline.sh, then sbatch pipeline.sh to launch the pipeline

Files and directories

• Snakefile : the pipeline itself
• activate_env.sh : activate the conda environement required to launch the pipeline
• config.yaml : config file to chose which reads, assemblers and evaluation methods to use
• initialise_env.sh : create the conda environement required to launch the pipeline and instal external dependencies
• np_pipeline.sh : a wraper to previsualise the pipeline execution
• pipeline.sh : a wraper to call the pipeline

assemblers :

Metagenome assemblers, and eventually polishers, or other programs that help to assemble a metagenome and are called by rules in assembly.smk.

assembly_evaluation :

Programs that evaluate the quality of a metagenome assembly and produce reports, with or without references, that are called by rules in assembly_evaluation.smk

binning_and_evaluation :

Programs that regroup metagenome contigs into bins, and evaluate them without, or eventually with, references, that are called by rules in binning_evaluation.smk

dependencies :

Programs that install dependencies that are not supported by conda, and where those dependencies are installed

env :

Conda environements used by various rules

rules :

Auxiliary snakefiles that contain rules for specific parts of the pipeline : assembly, evaluation of the assembly and binning with evaluation of the binning.

utils:

Unsupported files that are not directly involved in the pipeline, but might be (or have been) useful to prepare or analyze data. Most aren't up to date with the pipeline, but might be useful to specific application or for future developements.