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 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.
$ git clone https://github.com/cdeanj/snpfinder.git $ cd snpfinder $ make $ ./snpfinder
$ ./snpfinder [options]
Path to fasta formatted resistance database
$ -amr_fp /path/to/your/resistance_database.fasta
Path to single-end SAM formatted alignment file
$ -samse /path/to/your/single_alignment.sam
Path to paired-end SAM formatted alignment file
$ -sampe /path/to/your/paired_alignment.sam
Boolean flag for filtering on unique alignments
Output file path
$ -out_fp /path/to/your/output.txt