NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences

BMC Bioinformatics

Software

Geir Kjetil Sandve¹  Ksenia Khelik¹  Alexander Johan Nederbragt²  Torbjørn Rognes³  Karin Lagesen⁴ 

[1] Biomedical Informatics Research Group, Department of Informatics, University of Oslo, PO Box 1080, 0316, Oslo, Norway;Biomedical Informatics Research Group, Department of Informatics, University of Oslo, PO Box 1080, 0316, Oslo, Norway;Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway;Biomedical Informatics Research Group, Department of Informatics, University of Oslo, PO Box 1080, 0316, Oslo, Norway;Department of Microbiology, Oslo University Hospital, PO Box 4950 Nydalen, Rikshospitalet, 0424, Oslo, Norway;Biomedical Informatics Research Group, Department of Informatics, University of Oslo, PO Box 1080, 0316, Oslo, Norway;Norwegian Veterinary Institute, PO Box 750 Sentrum, 0106, Oslo, Norway;

关键词: Whole-genome alignment;    Comparative analysis;    Whole-genome assembly;    Annotation of differences;   

DOI  :  10.1186/s12859-017-1748-z

 received in 2016-09-23, accepted in 2017-07-04,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundComparing sets of sequences is a situation frequently encountered in bioinformatics, examples being comparing an assembly to a reference genome, or two genomes to each other. The purpose of the comparison is usually to find where the two sets differ, e.g. to find where a subsequence is repeated or deleted, or where insertions have been introduced. Such comparisons can be done using whole-genome alignments. Several tools for making such alignments exist, but none of them 1) provides detailed information about the types and locations of all differences between the two sets of sequences, 2) enables visualisation of alignment results at different levels of detail, and 3) carefully takes genomic repeats into consideration.ResultsWe here present NucDiff, a tool aimed at locating and categorizing differences between two sets of closely related DNA sequences. NucDiff is able to deal with very fragmented genomes, repeated sequences, and various local differences and structural rearrangements. NucDiff determines differences by a rigorous analysis of alignment results obtained by the NUCmer, delta-filter and show-snps programs in the MUMmer sequence alignment package. All differences found are categorized according to a carefully defined classification scheme covering all possible differences between two sequences. Information about the differences is made available as GFF3 files, thus enabling visualisation using genome browsers as well as usage of the results as a component in an analysis pipeline. NucDiff was tested with varying parameters for the alignment step and compared with existing alternatives, called QUAST and dnadiff.ConclusionsWe have developed a whole genome alignment difference classification scheme together with the program NucDiff for finding such differences. The proposed classification scheme is comprehensive and can be used by other tools. NucDiff performs comparably to QUAST and dnadiff but gives much more detailed results that can easily be visualized. NucDiff is freely available on https://github.com/uio-cels/NucDiff under the MPL license.

【 授权许可】

CC BY   
© The Author(s). 2017