De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application

BMC Bioinformatics
Wiktor Kuśmirek, Robert Nowak

Abstract

Many organisms, in particular bacteria, contain repetitive DNA fragments called tandem repeats. These structures are restored by DNA assemblers by mapping paired-end tags to unitigs, estimating the distance between them and filling the gap with the specified DNA motif, which could be repeated many times. However, some of the tandem repeats are longer than the distance between the paired-end tags. We present a new algorithm for de novo DNA assembly, which uses the relative frequency of reads to properly restore tandem repeats. The main advantage of the presented algorithm is that long tandem repeats, which are much longer than maximum reads length and the insert size of paired-end tags can be properly restored. Moreover, repetitive DNA regions covered only by single-read sequencing data could also be restored. Other existing de novo DNA assemblers fail in such cases. The presented application is composed of several steps, including: (i) building the de Bruijn graph, (ii) correcting the de Bruijn graph, (iii) normalizing edge weights, and (iv) generating the output set of DNA sequences. We tested our approach on real data sets of bacterial organisms. The software library, console application and web application were developed. We...Continue Reading

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Datasets Mentioned

BETA
SRR5431732
SRR1981622
SRR1981619

Methods Mentioned

BETA
PCR

Software Mentioned

QUAST
Boost
Illumina pair - end Read Simulator
bioweb
ABySS Velvet
SPAdes
Apache Spark
dnaasm application
Velvet
dnaasm

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