Abstract
Next-generation sequencing technologies have fostered an unprecedented proliferation of high-throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. In this context, an important issue is the need of a careful assessment of the accuracy of the assembly process. Here, we review the efficiency of a panel of assemblers, specifically designed to handle data from GS FLX 454 platform, on three bacterial data sets with different characteristics in terms of reads coverage and repeats content. Our aim is to investigate their strengths and weaknesses in the reconstruction of the reference genomes. In our benchmarking, we assess assemblers' performance, quantifying and characterizing assembly gaps and errors, and evaluating their ability to solve complex genomic regions containing repeats. The final goal of this analysis is to highlight pros and cons of each method, in order to provide the final user with general criteria for the right choice of the appropriate assembly strategy, depending on the specific needs. A further aspect we have explored is the relationship between coverage of a sequencing project and quality of the obtained results. The final outcome suggests that, for a good tradeoff between costs and results, the planned genome coverage of an experiment should not exceed 20-30 ×.
| Original language | English |
|---|---|
| Article number | bbr063 |
| Pages (from-to) | 269-280 |
| Number of pages | 12 |
| Journal | Briefings in Bioinformatics |
| Volume | 13 |
| Issue number | 3 |
| DOIs | |
| Publication status | Published - May 2012 |
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Keywords
- 454 pyrosequencing
- Assembly algorithm assessment
- Bacterial genome
- Coverage
ASJC Scopus subject areas
- Molecular Biology
- Information Systems
Cite this
Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data. / Finotello, Francesca; Lavezzo, Enrico; Fontana, Paolo; Peruzzo, Denis; Albiero, Alessandro; Barzon, Luisa; Falda, Marco; Di Camillo, Barbara; Toppo, Stefano.
In: Briefings in Bioinformatics, Vol. 13, No. 3, bbr063, 05.2012, p. 269-280.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data
AU - Finotello, Francesca
AU - Lavezzo, Enrico
AU - Fontana, Paolo
AU - Peruzzo, Denis
AU - Albiero, Alessandro
AU - Barzon, Luisa
AU - Falda, Marco
AU - Di Camillo, Barbara
AU - Toppo, Stefano
PY - 2012/5
Y1 - 2012/5
N2 - Next-generation sequencing technologies have fostered an unprecedented proliferation of high-throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. In this context, an important issue is the need of a careful assessment of the accuracy of the assembly process. Here, we review the efficiency of a panel of assemblers, specifically designed to handle data from GS FLX 454 platform, on three bacterial data sets with different characteristics in terms of reads coverage and repeats content. Our aim is to investigate their strengths and weaknesses in the reconstruction of the reference genomes. In our benchmarking, we assess assemblers' performance, quantifying and characterizing assembly gaps and errors, and evaluating their ability to solve complex genomic regions containing repeats. The final goal of this analysis is to highlight pros and cons of each method, in order to provide the final user with general criteria for the right choice of the appropriate assembly strategy, depending on the specific needs. A further aspect we have explored is the relationship between coverage of a sequencing project and quality of the obtained results. The final outcome suggests that, for a good tradeoff between costs and results, the planned genome coverage of an experiment should not exceed 20-30 ×.
AB - Next-generation sequencing technologies have fostered an unprecedented proliferation of high-throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. In this context, an important issue is the need of a careful assessment of the accuracy of the assembly process. Here, we review the efficiency of a panel of assemblers, specifically designed to handle data from GS FLX 454 platform, on three bacterial data sets with different characteristics in terms of reads coverage and repeats content. Our aim is to investigate their strengths and weaknesses in the reconstruction of the reference genomes. In our benchmarking, we assess assemblers' performance, quantifying and characterizing assembly gaps and errors, and evaluating their ability to solve complex genomic regions containing repeats. The final goal of this analysis is to highlight pros and cons of each method, in order to provide the final user with general criteria for the right choice of the appropriate assembly strategy, depending on the specific needs. A further aspect we have explored is the relationship between coverage of a sequencing project and quality of the obtained results. The final outcome suggests that, for a good tradeoff between costs and results, the planned genome coverage of an experiment should not exceed 20-30 ×.
KW - 454 pyrosequencing
KW - Assembly algorithm assessment
KW - Bacterial genome
KW - Coverage
UR - http://www.scopus.com/inward/record.url?scp=82255165034&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=82255165034&partnerID=8YFLogxK
U2 - 10.1093/bib/bbr063
DO - 10.1093/bib/bbr063
M3 - Article
C2 - 22021898
AN - SCOPUS:82255165034
VL - 13
SP - 269
EP - 280
JO - Briefings in Bioinformatics
JF - Briefings in Bioinformatics
SN - 1467-5463
IS - 3
M1 - bbr063
ER -