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Data released on November 24, 2015

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

Kaplinski, L; Lepamets, M; Remm, M (2015): Supporting materials and software for "GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists". GigaScience Database. http://dx.doi.org/10.5524/100178 RIS BibTeX Text

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.
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.

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Related manuscripts:

doi:10.1186/s13742-015-0097-y

Additional information:

https://github.com/bioinfo-ut/GenomeTester4

Keywords:

k-mers sequence analysis next-generation sequencing 

Software

http://gigadb.org/images/data/cropped/100178.jpg

Funding:

  • Funding body - Ministry of Education and Research
  • Location - Republic of Estonia
  • Award ID - SF0180026s09
  • Funding body - Ministry of Education and Research
  • Location - Republic of Estonia
  • Award ID - IUT34-11

Files: (FTP site) Table Settings

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File NameSample IDFile TypeFile FormatSizeRelease Date 
OtherUNKNOWN8.16 GB2015-11-02
TextTEXT149.48 KB2015-11-02
OtherUNKNOWN633.32 MB2015-11-02
OtherUNKNOWN44.28 MB2015-11-02
OtherTAR55.94 GB2015-11-02
ScriptUNKNOWN2.32 KB2015-11-02
ReadmeTEXT-0 KB2015-11-02
ScriptTAR2.38 KB2015-11-02
OtherUNKNOWN7.84 MB2015-11-02
OtherUNKNOWN921.92 KB2015-11-02
Displaying 1-10 of 16 File(s).

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