Paper Info
Title
Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns.
Abstract
With the advent of Next-Generation Sequencing technologies (NGS), a large amount of short read data has been generated. If a reference genome is not available, the assembly of a template sequence is usually challenging because of repeats and the short length of reads. When NGS reads cannot be mapped onto a reference genome alignment-based methods are not applicable. However it is still possible to study the evolutionary relationship of unassembled genomes based on NGS data.We present a parameter-free alignment-free method, called Under2, based on variable-length patterns, for the direct comparison of sets of NGS reads. We define a similarity measure using variable-length patterns, as well as reverses and reverse-complements, along with their statistical and syntactical properties. We evaluate several alignment-free statistics on the comparison of NGS reads coming from simulated and real genomes. In almost all simulations our method Under2 outperforms all other statistics. The performance gain becomes more evident when real genomes are used.The new alignment-free statistic is highly successful in discriminating related genomes based on NGS reads data. In almost all experiments, it outperforms traditional alignment-free statistics that are based on fixed length patterns.
Year
DOI
Venue
2014
10.1186/1471-2105-15-S9-S1
BMC Bioinformatics
Keywords
Field
DocType
bacteria,phylogeny,genomics,archaea,genome,algorithms
Genome,Hybrid genome assembly,Deep sequencing,Similarity measure,Biology,Genomics,DNA sequencing,Bioinformatics,Genetics,Reference genome,DNA microarray
Journal
Volume
Issue
ISSN
15 Suppl 9
S-9
1471-2105
Citations 
PageRank 
References 
7
0.47
20
Authors
2
Name
Order
Citations
PageRank
Matteo Comin119120.94
Michele Schimd2161.31