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Bioinformatics. 2014 May 1;30(9):1228-35. doi: 10.1093/bioinformatics/btu023. Epub 2014 Jan 17.

Exploring genome characteristics and sequence quality without a reference.

Author information

1
Ontario Institute for Cancer Research, Toronto, Canada.

Abstract

MOTIVATION:

The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to assisting the user with the assembly.

RESULTS:

This article addresses the practical aspects of de novo assembly by introducing new ways to perform quality assessment on a collection of sequence reads. The software implementation calculates per-base error rates, paired-end fragment-size distributions and coverage metrics in the absence of a reference genome. Additionally, the software will estimate characteristics of the sequenced genome, such as repeat content and heterozygosity that are key determinants of assembly difficulty.

PMID:
24443382
PMCID:
PMC3998141
DOI:
10.1093/bioinformatics/btu023
[Indexed for MEDLINE]
Free PMC Article

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