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fasta_reader.cpp
fasta_reader.hpp
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snip_writer.cpp
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README.md

SNPFinder

Overview

SNPFinder is a simple alignment-based haplotype variant caller that can be used with metagenomic sequence data. Input to SnipFinder is a SAM formatted alignment file and a FASTA formatted reference database.

Output

Output is a single TSV formatted text file with three columns: Gene, Haplotype Pattern, and Occurrence. The gene corresponds to the reference sequence for which haplotypes were identified within a single or read-pair. The haplotype pattern is the haplotype sequence identified within a single or read-pair. Occurrence is the number of times the current haplotype pattern was identified within a target reference sequence.

Installation

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

Usage

$ ./snpfinder [options]

Options

-amr_fp

Path to fasta formatted resistance database

$ -amr_fp /path/to/your/resistance_database.fasta
-samse

Path to single-end SAM formatted alignment file

$ -samse /path/to/your/single_alignment.sam
-sampe

Path to paired-end SAM formatted alignment file

$ -sampe /path/to/your/paired_alignment.sam
-b

Boolean flag for filtering on unique alignments

$ -b
-out_fp

Output file path

$ -out_fp /path/to/your/output.txt