Abstract
Recent studies have demonstrated the capability of second generation sequencing (SGS)
to provide coverage of short tandem repeats (STRs) found within the human genome.
However, there are relatively few bioinformatic software packages capable of detecting
these markers in the raw sequence data. The extant STR-calling tools are sophisticated,
but are not always applicable to the analysis of the STR loci commonly used in forensic
analyses. STRait Razor is a newly developed Perl-based software tool that runs on
the Linux/Unix operating system and is designed to detect forensically-relevant STR
alleles in FASTQ sequence data, based on allelic length. It is capable of analyzing
STR loci with repeat motifs ranging from simple to complex without the need for extensive
allelic sequence data. STRait Razor is designed to interpret both single-end and paired-end
data and relies on intelligent parallel processing to reduce analysis time. Users
are presented with a number of customization options, including variable mismatch
detection parameters, as well as the ability to easily allow for the detection of
alleles at new loci. In its current state, the software detects alleles for 44 autosomal
and Y-chromosome STR loci. The study described herein demonstrates that STRait Razor
is capable of detecting STR alleles in data generated by multiple library preparation
methods and two Illumina® sequencing instruments, with 100% concordance. The data also reveal noteworthy concepts
related to the effect of different preparation chemistries and sequencing parameters
on the bioinformatic detection of STR alleles.
Keywords
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Article info
Publication history
Accepted:
April 15,
2013
Received in revised form:
April 4,
2013
Received:
March 8,
2013
Identification
Copyright
© 2013 Elsevier Ireland Ltd. Published by Elsevier Inc. All rights reserved.
