BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data

Juntao Liu; Guojun Li; Zheng Chang; Ting Yu; Bingqiang Liu; Rick McMullen; Pengyin Chen; Xiuzhen Huang

doi:10.1371/journal.pcbi.1004772

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Open Access

Peer-reviewed

Research Article

BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data

Juntao Liu ,

Contributed equally to this work with: Juntao Liu, Guojun Li

Affiliation School of Mathematics, Shandong University, Jinan, China
⨯
Guojun Li ,

Contributed equally to this work with: Juntao Liu, Guojun Li

* E-mail: guojunsdu@gmail.com (GL); xhuang@astate.edu (XH)

Affiliation School of Mathematics, Shandong University, Jinan, China
⨯
Zheng Chang,

Affiliation School of Mathematics, Shandong University, Jinan, China
⨯
Ting Yu,

Affiliation School of Mathematics, Shandong University, Jinan, China
⨯
Bingqiang Liu,

Affiliation School of Mathematics, Shandong University, Jinan, China
⨯
Rick McMullen,

Affiliation High Performance Computing Center, University of Arkansas, Fayetteville, Arkansas, United States of America
⨯
Pengyin Chen,

Affiliation Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
⨯
Xiuzhen Huang

* E-mail: guojunsdu@gmail.com (GL); xhuang@astate.edu (XH)

Affiliation Department of Computer Science, Arkansas State University, Jonesboro, Arkansas, United States of America
⨯

BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data

Juntao Liu,
Guojun Li,
Zheng Chang,
Ting Yu,
Bingqiang Liu,
Rick McMullen,
Pengyin Chen,
Xiuzhen Huang

Published: February 19, 2016
https://doi.org/10.1371/journal.pcbi.1004772

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Uses a single core....?!

Posted by djackson on 21 Mar 2018 at 13:56 GMT

In addition to the issues raised by macmanes this assembler apparently can only use a single core (no option to compile it to run under mpi either)..... weird?

No competing interests declared.

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BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data

BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data

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Uses a single core....?!

Posted by djackson on 21 Mar 2018 at 13:56 GMT