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README.md
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annotation_reader.hpp
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resistome.cpp
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utility.hpp

README.md

Resistome Analyzer

Overview

Resistome Analyzer is a simple tool for analyzing the resistome of large metagenomic dataets. This program takes in as input a SAM formatted alignment file, a FASTA formatted reference database, and a CSV formatted annotation database. The alignment file is treated as the sample resistome. This is done by counting each alignment for each target gene found in the alignment file.

Output

The output consists of four TSV text files, one for each level of the annotation database hierarchy (gene, group, mechanism, class). Within each file, the first column lists the sample that was analyzed (SAM file), the second column lists the gene, group, mechanism or class that was identified, and the third column gives the total count of reads that aligned to the target gene, group, mechanism or class. For the gene-level output, there is a fourth column that describes the gene fraction, which can be defined as the proportion of nucleotides in the reference sequence that were aligned to by at least one sequence read. This threshold is user-defined, however, it is recommended to set this parameter to a value of 80 in order to decrease the amount of false positive gene identifications.

Installation

$ git clone https://github.com/cdeanj/resistomeanalyzer.git
$ cd resistomeanalyzer
$ make
$ ./resistome

Usage

$ ./resistome \
   -ref_fp ref.fa \
   -sam_fp alignments.sam \
   -annot_fp annotations.csv \
   -gene_fp gene.tsv \
   -group_fp group.tsv \
   -class_fp class.tsv \
   -mech_fp mech.tsv \
   -t 80

Options

Option Type Description
ref_fp FILE Path to FASTA formatted reference database (each sequence must be on a single line)
annot_fp FILE Path to CSV formatted annotation database
sam_fp FILE Path to SAM formatted alignment file
gene_fp FILE File to write gene level results to
group_fp FILE File to write group level results to
class_fp FILE File to write class level results to
mech_fp FILE File to write mechanism level results to
t INT Threshold to determine gene significance