GT-Pro

Ultra-rapid metagenotyping of the human gut microbiome. GT-Pro - the GenoTyper for PROkaryotes. Ultra-rapid genotyping of prokaryotes in shotgun metagenomes. To genotype a microbiome, GT-Pro takes as input one or more shotgun metagenomics sequencing libraries in FASTQ format. It returns counts of reads exactly matching each allele of each SNP in a concise table-shaped format for its output, with one row for each bi-allelic SNP site that has exactly 8 fields: species, SNP ID, contig, contig position, allele 1, allele 2 and coverage of allele 1 and coverage of allele 2. The k-mer exact match based genotyping algorithm is optimized for machine specificiations, and it can run on a personal computer.