Workshop: Graph compression approaches in assembly

Jason Pell; Arend Hintze; Rosangela Canino-Koning; Adina Howe; James M. Tiedje; Charles Brown

doi:10.1109/ICCABS.2012.6182675

Workshop: Graph compression approaches in assembly

Jason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje, Charles Brown

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

Using a probabilistic data structure to store DNA assembly graphs results in a significant memory savings over other methods. As long as the Bloom filter remains below a specific false positive rate, it remains possible to traverse the graph. Using a Bloom filter has many applications in metagenomics, mRNAseq, read filtering, and error correction. We are currently exploring these possibilities and more.

Original language	English (US)
Title of host publication	2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012
DOIs	https://doi.org/10.1109/ICCABS.2012.6182675
State	Published - May 8 2012
Externally published	Yes
Event	2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012 - Las Vegas, NV, United States Duration: Feb 23 2012 → Feb 25 2012

Other

Other	2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012
Country/Territory	United States
City	Las Vegas, NV
Period	2/23/12 → 2/25/12

Keywords

Bloom filters
de Bruijn graphs
k-mers
metagenomics
next-generation sequencing

ASJC Scopus subject areas

Biomedical Engineering
Applied Mathematics

Access to Document

10.1109/ICCABS.2012.6182675

Cite this

Pell, J, Hintze, A, Canino-Koning, R, Howe, A, Tiedje, JM & Brown, C 2012, Workshop: Graph compression approaches in assembly. in 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012., 6182675, 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012, Las Vegas, NV, United States, 2/23/12. https://doi.org/10.1109/ICCABS.2012.6182675

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author = "Jason Pell and Arend Hintze and Rosangela Canino-Koning and Adina Howe and Tiedje, {James M.} and Charles Brown",

year = "2012",

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doi = "10.1109/ICCABS.2012.6182675",

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AU - Howe, Adina

AU - Tiedje, James M.

AU - Brown, Charles

PY - 2012/5/8

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KW - de Bruijn graphs

KW - k-mers

KW - metagenomics

KW - next-generation sequencing

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BT - 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012

Y2 - 23 February 2012 through 25 February 2012

ER -

Workshop: Graph compression approaches in assembly

Abstract

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Keywords

ASJC Scopus subject areas

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