Artificial_metagenomes_randomize

pipeline to generate artificial metagenomes randomized on the composition

The complete pipeline will generate K artificial metagenomes of a given sequencing depth (Nb of reads). The number of organisms in each metagenome is defined by the user in the abundance vector input. If the number of organism is set lower than the total number of organisms in the genome list, each artificial metagenome will randomly select a set of organisms. The abundance of each organisms in the metagenome follows an abundance vector defined by the user. The association of each organism to an abundance is randomized.

Requirements

Python 3

This pipeline necessites Python3 as well as several packages : -[numpy] (https://www.numpy.org/) -[Sklearn] (https://scikit-learn.org/stable/)

InSilicoSeq

Quick start

Edit scripts/config.sh file

please modify the following attributes

parameters

• NB_READS : nb reads to generate
• NB_METAGENOMES : nb metagenomes to generate
• MODEL : error/length model to use

You can also modify

• BIN = change for your own bin directory.
• MAIL_TYPE = change the mail type option. By default set to "bea".
• QUEUE = change the submission queue. By default set to "standard".

Run pipeline

Run

./submit.sh

This command will place two jobs in queue.