FAMA

Introduction

Fama is a fast pipeline for functional and taxonomic analysis of shotgun metagenomic sequences.

Installation

If you want to install FAMA on your own, follow these instructions in the FAMA manual.

Available on Crunchomics: Yes, via the metatools share. For access contact Anna Heintz Buschart a.u.s.heintzbuschart@uva.nl

Instructions

#activate environment
conda activate /zfs/omics/projects/metatools/TOOLS/miniconda3/envs/FAMA

#get template and add 
#(if you downloaded FAMA by yourself then the ini file can be found in the folder you downloaded)
cp /zfs/omics/projects/metatools/DB/fama_new/project.ini.sample Annotations/Fama/my.project.config

#run FAMA 
python3 /zfs/omics/projects/metatools/DB/fama_new/py/fama.py -c /zfs/omics/projects/metatools/DB/fama_new/config.ini -p my.project.config

Example content of Annotations/Fama/my.project.config:

[DEFAULT]
project_name = 'Test sample sulfur'
collection = test_sulfur_v1
ref_output_name = ref_tabular_output.txt
background_output_name = bgr_tabular_output.txt
ref_hits_list_name = ref_hits.txt
ref_hits_fastq_name = ref_hits.fq
reads_fastq_name = reads.fq
pe_reads_fastq_name = reads_pe.fq
output_subdir = out_sulfur
report_name = report.txt
xml_name = krona.xml
html_name = functional_profile.html
reads_json_name = reads.json
assembly_subdir = assembly
work_dir = /zfs/omics/projects/thiopac-mgx/nina_wdir/Annotations/Fama

[test_sample]
sample_id = TPS_fame_sulfur
fastq_pe1 = /zfs/omics/projects/thiopac-mgx/nina_wdir/faa/All_genomes.faa
sample_dir = /zfs/omics/projects/thiopac-mgx/nina_wdir/Annotations/Fama
replicate = 0
#fastq_pe1_readcount = 30
#fastq_pe1_basecount = 4509
#fastq_pe2_readcount = 30
#fastq_pe2_basecount = 4346
#rpkg_scaling = 0.18962061540779365
#insert_size = 233.4950097660472

Adding more databases to FAMA

It is possible to add new databases to FAMA. Below is an example on how to add a custom sulfur database.

Sulfur database installation instructions:

Download and unpack the archive into a separate directory:https://iseq.lbl.gov/mydocs/fama_downloads/fama_sulfur_dataset.tar.gz
Create diamond databases:

diamond makedb --in classification_database.faa --db classification_database
diamond makedb --in selection_database_clustered.faa --db selection_database

Append your config.ini file with a new section and replace “” with real paths:

[test_sulfur_v1]
functions_file = <path to db files>/collection_functions.txt
taxonomy_file = <path to db files>/collection_taxonomy.txt
reference_diamond_db = <path to db files>/selection_database.dmnd
background_diamond_db = <path to db files>/classification_database.dmnd
reference_db_size = 6990766
background_db_size = 99120132