parseMethods Module

---

Welcome to the parseMethods module! This module takes a directory containing output files from several metagenomics software and creates a standard table (with the full lineage and read/proportions) that can be easily imported into R for downstream analyses. parseMethods is part of SEPA, a modular pipeline for testing metagenomic profiling software using simulations. Currently, parseMethods can process result files from pathoscope2, metamix, sigma, metaphlan2 (under development), and constrains (metaphlan dependent)

Requirements

Bash version 4 (comes with Linux and MacOSX) Rscript (R statistical framework) 3.0 and greater (download here) R packages rJava, methods, xlsxjars (install from R console by issuing install.packages(c("rJava", "methods", "xlsxjars")))

Usage

bash parseMethods.bash --workpath . --cfile config.conf
or
bash parseMethods.bash --workpath . --method PATHOSCOPE

Where --workpath is the path to the directory that contains your program-specific output files. In the example, the files within ./example_files/ come from PathoScope2. --cfile is a plain-text configuration file where you can pass options to the program as to what piece of software the files come from, whether you want proportions instead of reads, etc. finally --method can avoid you to use an config file just passing the method (coma separate), only valid for pathoscope2, metamix, and kraken, taxator and centrifuge.

Example output

Superkingdom	Phylum	Class	Order	Family	Genus	Specie	Name	ti	ID1000-sam	ID150-sam	ID300-sam	ID75-sam
Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	Bacillus anthracis	Bacillus anthracis str. CDC 684	568206	157496	155096	156413	157488
Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	Bacillus anthracis	Bacillus anthracis str. Ames	198094	1672	0	0	123
Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	Bacillus anthracis	Bacillus anthracis str. Sterne	260799	10	0	0	0
Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus	Bacillus anthracis	Bacillus anthracis str. H9401	768494	0	0	0	1437
Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus	Streptococcus pneumoniae	Streptococcus pneumoniae TCH8431/19A	525381	5556	5362	5244	5266
Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus	Streptococcus pneumoniae	Streptococcus pneumoniae ST556	1130804	20	0	0	0
Bacteria	Actinobacteria	Actinobacteria	Propionibacteriales	Propionibacteriaceae	Propionibacterium	Propionibacterium acnes	Propionibacterium acnes KPA171202	267747	5544	5373	5320	5504
Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	Lactobacillus crispatus	Lactobacillus crispatus ST1	748671	0	5689	5586	5586
Bacteria	Actinobacteria	Actinobacteria	Corynebacteriales	Mycobacteriaceae	Mycobacterium	Mycobacterium tuberculosis	Mycobacterium tuberculosis CDC1551	83331	0	12958	12758	12946
Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus	Streptococcus anginosus	Streptococcus anginosus C238	862971	0	5850	5648	5887
Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	Staphylococcus epidermidis	Staphylococcus epidermidis RP62A	176279	0	4349	4248	4314
Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	Lactobacillus rhamnosus	Lactobacillus rhamnosus ATCC 8530	1088720	0	741	624	707
Bacteria	Actinobacteria	Actinobacteria	Propionibacteriales	Propionibacteriaceae	Propionibacterium	Propionibacterium acnes	Propionibacterium acnes 6609	1031709	0	0	0	3
Bacteria	Actinobacteria	Actinobacteria	Corynebacteriales	Mycobacteriaceae	Mycobacterium	Mycobacterium tuberculosis	Mycobacterium tuberculosis KZN 605	478435	0	0	0	164
Bacteria	Actinobacteria	Actinobacteria	Corynebacteriales	Mycobacteriaceae	Mycobacterium	Mycobacterium tuberculosis	Mycobacterium tuberculosis H37Ra	419947	0	0	0	9
Bacteria	Actinobacteria	Actinobacteria	Corynebacteriales	Mycobacteriaceae	Mycobacterium	Mycobacterium tuberculosis	Mycobacterium tuberculosis H37Rv	83332	0	0	0	2

Citation

Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA, Johnson WE.
PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples Microbiome 2014 Dec 1;2(1):1-5. PMID: 25225611

Morfopoulou S, Plagnol V.
Bayesian mixture analysis for metagenomic community profiling
Bioinformatics 2015 May 21:btv317. PMID: 26002885

Ahn TH, Chai J, Pan C.
Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance
Bioinformatics 2014 Sep 29:btu641. PMID: 25266224

Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N.
MetaPhlAn2 for enhanced metagenomic taxonomic profiling Nature methods 2015 Oct 1;12(10):902-3. PMID: 26418763

Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D.
ConStrains identifies microbial strains in metagenomic datasets
Nature biotechnology 2015 Oct 1;33(10):1045-52. PMID: 26344404