aponsero / lichen_mock_metagenomes

Pipeline to generate mock lichen metagenomes. Parralelized for a HPC use

lichen_mock_metagenomes

Pipeline to generate mock contig lichen metagenomes. Parralelized for a HPC use

This pipeline grind complete metagenomes into custom contig size (./grind.sh) then subset these sequences into chose proportions to mimic a lichen metagenome (./get_mocks.sh).

Requirements

Perl 5.010

This pipeline requires perl 5.010 and the package Bioperl installed

Python3

This pipeline requires python 3 and the following packages :

• argparse
• itertools
• Biopython
• random

Quick start

Edit scripts/config.sh file

please modify the

• FUNGI_DIR= path to directory containing the fungi genomes

• ALGAE_DIR= path to directory containing the algae genomes

• BACT_DIR= path to directory containing the prokaryotic genomes

• VIR_DIR=path to directory containing the viral genomes

• FUNGI_PERCENT= % of fungi contig in the final mock community

• ALGAE_PERCENT= % of algae contig in the final mock community

• BACT_PERCENT= % of prokaryotic contig in the final mock community

• VIR_PERCENT= % of viral contig in the final mock community

• NB_READS=number of sequences in the final mock community

• NB_MOCK=number of required mock communities

• SIZE_CONTIGS=size in bp of the sequences in the mock communities

• OUT= path to output directory

• 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

./grind.sh

This command will place one job in queue. Once the job is completed, run:

./get_mocks.sh

This command will place one job in queue.