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Cookiecutter: a tool for kmer-based read filtering and extraction

Ekaterina Starostina, Gaik Tamazian, Pavel Dobrynin, Stephen O’Brien, Aleksey Komissarov
doi: https://doi.org/10.1101/024679
Ekaterina Starostina
1Bioinformatics Institute, St. Petersburg, Russia
2Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
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Gaik Tamazian
3Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41A Sredniy Avenue, 198207, St. Petersburg, Russia
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Pavel Dobrynin
3Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41A Sredniy Avenue, 198207, St. Petersburg, Russia
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Stephen O’Brien
3Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41A Sredniy Avenue, 198207, St. Petersburg, Russia
4Oceanographic Center, Nova Southeastern University Ft Lauderdale, 8000 N. Ocean Drive, Ft Lauderdale, Florida 33004, USA
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Aleksey Komissarov
3Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41A Sredniy Avenue, 198207, St. Petersburg, Russia
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Abstract

Motivation Kmer-based analysis is a powerful method used in read error correction and implemented in various genome assembly tools. A number of read processing routines include extracting or removing sequence reads from the results of high-throughput sequencing experiments prior to further analysis. Here we present a new approach to sorting or filtering of raw reads based on a provided list of kmers.

Results We developed Cookiecutter — a computational tool for rapid read extraction or removing according to a provided list of k-mers generated from a FASTA file. Cookiecutter is based on the implementation of the Aho-Corasik algorithm and is useful in routine processing of high-throughput sequencing datasets. Cookiecutter can be used for both removing undesirable reads and read extraction from a user-defined region of interest.

Availability The open-source implementation with user instructions can be obtained from GitHub: https://github.com/ad3002/Cookiecutter.

Footnotes

  • ↵* ad3002{at}gmail.com

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted August 16, 2015.
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Cookiecutter: a tool for kmer-based read filtering and extraction
Ekaterina Starostina, Gaik Tamazian, Pavel Dobrynin, Stephen O’Brien, Aleksey Komissarov
bioRxiv 024679; doi: https://doi.org/10.1101/024679
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Cookiecutter: a tool for kmer-based read filtering and extraction
Ekaterina Starostina, Gaik Tamazian, Pavel Dobrynin, Stephen O’Brien, Aleksey Komissarov
bioRxiv 024679; doi: https://doi.org/10.1101/024679

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