IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels

IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels

Motivation: RNA sequencing based on next-generation sequencing technology is effective for analyzing transcriptomes. Like de novo genome assembly, de novo transcriptome assembly does not rely on any reference genome or additional annotation information, but is more difficult. In particular, isoforms...

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Main Authors: Peng, Yu, Leung, Henry C. M., Yiu, Siu-Ming, Lv, Ming-Ju, Zhu, Xin-Guang, Chin, Francis Y. L.
Format: Online
Language:English
Published: Oxford University Press 2013
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694675/
id pubmed-3694675
recordtype oai_dc
spelling pubmed-36946752013-06-27 IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels Peng, Yu Leung, Henry C. M. Yiu, Siu-Ming Lv, Ming-Ju Zhu, Xin-Guang Chin, Francis Y. L. Ismb/Eccb 2013 Proceedings Papers Committee July 21 to July 23, 2013, Berlin, Germany Motivation: RNA sequencing based on next-generation sequencing technology is effective for analyzing transcriptomes. Like de novo genome assembly, de novo transcriptome assembly does not rely on any reference genome or additional annotation information, but is more difficult. In particular, isoforms can have very uneven expression levels (e.g. 1:100), which make it very difficult to identify low-expressed isoforms. One challenge is to remove erroneous vertices/edges with high multiplicity (produced by high-expressed isoforms) in the de Bruijn graph without removing correct ones with not-so-high multiplicity from low-expressed isoforms. Failing to do so will result in the loss of low-expressed isoforms or having complicated subgraphs with transcripts of different genes mixed together due to erroneous vertices/edges. Oxford University Press 2013-07-01 2013-06-19 /pmc/articles/PMC3694675/ /pubmed/23813001 http://dx.doi.org/10.1093/bioinformatics/btt219 Text en © The Author 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Peng, Yu
Leung, Henry C. M.
Yiu, Siu-Ming
Lv, Ming-Ju
Zhu, Xin-Guang
Chin, Francis Y. L.
spellingShingle Peng, Yu
Leung, Henry C. M.
Yiu, Siu-Ming
Lv, Ming-Ju
Zhu, Xin-Guang
Chin, Francis Y. L.
IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels
author_facet Peng, Yu
Leung, Henry C. M.
Yiu, Siu-Ming
Lv, Ming-Ju
Zhu, Xin-Guang
Chin, Francis Y. L.
author_sort Peng, Yu
title IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels
title_short IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels
title_full IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels
title_fullStr IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels
title_full_unstemmed IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels
title_sort idba-tran: a more robust de novo de bruijn graph assembler for transcriptomes with uneven expression levels
description Motivation: RNA sequencing based on next-generation sequencing technology is effective for analyzing transcriptomes. Like de novo genome assembly, de novo transcriptome assembly does not rely on any reference genome or additional annotation information, but is more difficult. In particular, isoforms can have very uneven expression levels (e.g. 1:100), which make it very difficult to identify low-expressed isoforms. One challenge is to remove erroneous vertices/edges with high multiplicity (produced by high-expressed isoforms) in the de Bruijn graph without removing correct ones with not-so-high multiplicity from low-expressed isoforms. Failing to do so will result in the loss of low-expressed isoforms or having complicated subgraphs with transcripts of different genes mixed together due to erroneous vertices/edges.
publisher Oxford University Press
publishDate 2013
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694675/
_version_ 1611990059222827008

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