aponsero / Artificial_metagenomes_variableSize

Pipeline for the generation of artificial metagenomes containing a variable number of organisms. Parrallelized for HPC.

Artificial_metagenomes_variableSize

Pipeline for the generation of artificial metagenomes containing a variable number of organisms. Parrallelized for HPC.

The complete pipeline will generate K artificial metagenomes of a given sequencing depth (Nb of reads). The number of organisms in each metagenome is randomly chosen between a min and a max (defined by the user). IF SQUEUE is set to TRUE : the abundance distribution will be squeued. 1/5 of the organisms will represent around 60% of the total population. If SQUEUE is set to FALSE : The abundance of each organisms in the metagenome is obtained by dividing the total number of reads by the number of organisms, the addition of a gaussian noise and a normalization.

Requirements

Python 3

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

GemSim

This pipeline necessites to download and install GemSim on the HPC.

Quick start

Edit scripts/config.sh file

please modify the following attributes

• GEMSIM : path to the gemsim directory
• LIST_GENOMES : list of genomes that will constitute the artificial metagenomes
• GENOMES_DIR : path to the directory where the genomes are stored, Beware GemSim won't work if this is not relative to $GEMSIM
• RESULT_DIR : path to the output directory
• REL_OUT : relative path to the output dir for GEMSIM

parameters

• NB_READS : nb reads to generate

• NB_METAGENOMES : nb metagenomes to generate

• MODEL : error/length model to use

• MINI : nb minimum of organisms in the metagenomes

• MAXI : nb maximum of organisms in the metagenomes

• SQUEUE : If set to TRUE, the abundance distribution will be squeued. 1/5 of the organisms will represent around 60% of the total population. If set to FALSE, the abundance distribution of the organisms will be almost homogeneous.

• OUTNAME : indicate here the name to use for the output files

• MAIL_USER : indicate here your arizona.edu email

• GROUP : indicate here your group affiliation

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.