TransLiG: a de novo transcriptome assembler that uses line graph iteration

We present TransLiG, a new de novo transcriptome assembler, which is able to integrate the sequence depth and pair-end information into the assembling procedure by phasing paths and iteratively constructing line graphs starting from splicing graphs. TransLiG is shown to be significantly superior to...

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Detalles Bibliográficos
Autores principales: Liu, Juntao, Yu, Ting, Mu, Zengchao, Li, Guojun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6480747/
https://www.ncbi.nlm.nih.gov/pubmed/31014374
http://dx.doi.org/10.1186/s13059-019-1690-7
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author Liu, Juntao
Yu, Ting
Mu, Zengchao
Li, Guojun
author_facet Liu, Juntao
Yu, Ting
Mu, Zengchao
Li, Guojun
author_sort Liu, Juntao
collection PubMed
description We present TransLiG, a new de novo transcriptome assembler, which is able to integrate the sequence depth and pair-end information into the assembling procedure by phasing paths and iteratively constructing line graphs starting from splicing graphs. TransLiG is shown to be significantly superior to all the salient de novo assemblers in both accuracy and computing resources when tested on artificial and real RNA-seq data. TransLiG is freely available at https://sourceforge.net/projects/transcriptomeassembly/files/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1690-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-64807472019-05-01 TransLiG: a de novo transcriptome assembler that uses line graph iteration Liu, Juntao Yu, Ting Mu, Zengchao Li, Guojun Genome Biol Method We present TransLiG, a new de novo transcriptome assembler, which is able to integrate the sequence depth and pair-end information into the assembling procedure by phasing paths and iteratively constructing line graphs starting from splicing graphs. TransLiG is shown to be significantly superior to all the salient de novo assemblers in both accuracy and computing resources when tested on artificial and real RNA-seq data. TransLiG is freely available at https://sourceforge.net/projects/transcriptomeassembly/files/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1690-7) contains supplementary material, which is available to authorized users. BioMed Central 2019-04-23 /pmc/articles/PMC6480747/ /pubmed/31014374 http://dx.doi.org/10.1186/s13059-019-1690-7 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Liu, Juntao
Yu, Ting
Mu, Zengchao
Li, Guojun
TransLiG: a de novo transcriptome assembler that uses line graph iteration
title TransLiG: a de novo transcriptome assembler that uses line graph iteration
title_full TransLiG: a de novo transcriptome assembler that uses line graph iteration
title_fullStr TransLiG: a de novo transcriptome assembler that uses line graph iteration
title_full_unstemmed TransLiG: a de novo transcriptome assembler that uses line graph iteration
title_short TransLiG: a de novo transcriptome assembler that uses line graph iteration
title_sort translig: a de novo transcriptome assembler that uses line graph iteration
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6480747/
https://www.ncbi.nlm.nih.gov/pubmed/31014374
http://dx.doi.org/10.1186/s13059-019-1690-7
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AT muzengchao transligadenovotranscriptomeassemblerthatuseslinegraphiteration
AT liguojun transligadenovotranscriptomeassemblerthatuseslinegraphiteration

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