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Gigascience. 2015 Dec 3;4:58. doi: 10.1186/s13742-015-0097-y. eCollection 2015.

GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists.

Author information

1
Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu, 51010 Estonia.
2
Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia.

Abstract

BACKGROUND:

K-mer-based methods of genome analysis have attracted great interest because they do not require genome assembly and can be performed directly on sequencing reads. Many analysis tasks require one to compare k-mer lists from different sequences to find words that are either unique to a specific sequence or common to many sequences. However, no stand-alone k-mer analysis tool currently allows one to perform these algebraic set operations.

FINDINGS:

We have developed the GenomeTester4 toolkit, which contains a novel tool GListCompare for performing union, intersection and complement (difference) set operations on k-mer lists. We provide examples of how these general operations can be combined to solve a variety of biological analysis tasks.

CONCLUSIONS:

GenomeTester4 can be used to simplify k-mer list manipulation for many biological analysis tasks.

KEYWORDS:

K-mers; Next-generation sequencing; Sequence analysis

PMID:
26640690
PMCID:
PMC4669650
DOI:
10.1186/s13742-015-0097-y
[Indexed for MEDLINE]
Free PMC Article

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