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Title: k-merSNP discovery: Software for alignment-and reference-free scalable SNP discovery, phylogenetics, and annotation for hundreds of microbial genomes

With the flood of whole genome finished and draft microbial sequences, we need faster, more scalable bioinformatics tools for sequence comparison. An algorithm is described to find single nucleotide polymorphisms (SNPs) in whole genome data. It scales to hundreds of bacterial or viral genomes, and can be used for finished and/or draft genomes available as unassembled contigs or raw, unassembled reads. The method is fast to compute, finding SNPs and building a SNP phylogeny in minutes to hours, depending on the size and diversity of the input sequences. The SNP-based trees that result are consistent with known taxonomy and trees determined in other studies. The approach we describe can handle many gigabases of sequence in a single run. The algorithm is based on k-mer analysis.
Publication Date:
OSTI Identifier:
Report Number(s):
KSNP3; 003246WKSTN00
DOE Contract Number:
Software Revision:
Software Package Number:
Software Package Contents:
Media Directory; Software Abstract; Media includes Source Code; / 1 CD-ROM
Software CPU:
Open Source:
Source Code Available:
Research Org:
Lawrence Livermore National Laboratory
Sponsoring Org:
United States Department of Energy
Contributing Orgs:
S. N. Gardner, B. G. Hall
Country of Publication:
United States

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