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From Short to Long Reads: Benchmarking Assembly Tools (CROSBI ID 597213)

Prilog sa skupa u zborniku | sažetak izlaganja sa skupa | međunarodna recenzija

Sović, Ivan ; Skala, Karolj ; Šikić, Mile From Short to Long Reads: Benchmarking Assembly Tools // ISMB/ECCB 2013. 2013. str. 1-1

Podaci o odgovornosti

Sović, Ivan ; Skala, Karolj ; Šikić, Mile

engleski

From Short to Long Reads: Benchmarking Assembly Tools

An increasing number of DNA de novo assembly tools are being developed, each claiming to produce better results in some aspect than their competition. It is, however, interesting that not enough attention has been paid to their comparative evaluation. Even in cases where the quality of their results has been tested, it is hard to find information on their execution performance. We designed a benchmarking methodology and applied it to several DNA de novo assembly tools. Unlike other comparative studies, our primary goal was to focus on assemblers’ resource consumption as a function of varying lengths and coverages of input read sequences. Since such study is very time consuming, we have currently performed benchmarking on a limited number of assemblers, and report here the preliminary results. We have defined a collection of 77 datasets of simulated read sequences of E. Coli, designed to cover the space of varying read lengths and coverages. Benchmarking was performed on two de Bruijn graph (DBG) based assemblers, Velvet and SOAPdenovo, and two overlap graph (OG) based assemblers, SGA and Minimus. Preliminary results show that DBG-based assemblers generally perform faster than OG-based ones. Additionally, DBGs memory consumption reaches a plateau at some point. The two tested OGs produce differing memory results, presumably because of different underlying alignment algorithms. However, DBGs seem to produce much lower N50 and maximal contig lengths than OGs, especially for longer reads. We conclude that OG is the approach of preference for the upcoming sequencing technologies that will produce longer reads.

DNA ; sequencing ; assembly ; tools ; long read ; benchmark ; N50 ; performan ce

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Podaci o prilogu

1-1.

2013.

objavljeno

Podaci o matičnoj publikaciji

ISMB/ECCB 2013

Podaci o skupu

ISMB/ECCB 2013

poster

20.07.2013-24.07.2013

Berlin, Njemačka

Povezanost rada

Biologija, Računarstvo