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BinPacker specifications

Information


Unique identifier OMICS_11199
Name BinPacker
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Xiuzhen Huang <>

Publication for BinPacker

BinPacker in pipeline

2017
PMCID: 5394691
PMID: 28417958
DOI: 10.1038/srep45125

[…] were error corrected using rcorrector version 1.0.2. adapters, as well as bases with a phred score <2 were trimmed using skewer 0.2.2, and assembly was carried out using trinity version 2.2.0, binpacker version 1.0, and shannon version 0.0.2, after which the resultant transcriptomes were merged using the software package transfuse version 0.5.0 (https://github.com/cboursnell/transfuse). […]


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BinPacker in publications

 (5)
PMCID: 5700045
PMID: 29167578
DOI: 10.1038/s41598-017-16371-9

[…] 0.32 (https://goo.gl/vlhjev) following recommendations from. reads from each color morph were assembled together to create a joint assembly of coral transcripts using trinity version 2.20 and binpacker version 1.0.0, on a linux workstation with 64 cores and 1tb ram (https://goo.gl/q8pwuu). we used flags to indicate the stranded nature of sequencing reads and set the maximum allowable […]

PMCID: 5585965
PMID: 28874116
DOI: 10.1186/s12864-017-4101-z

[…] discovery rate (fdr) of 1%, using the benjamini-hochberg method for multiple testing correction., as no reference genome sequence exists for neotoma stephensi, we used a novel de novo algorithm, binpacker [], to assemble a foregut reference transcriptome. the sequence input was 45,992,608 composite reads from the 3 n. stephensi foregut libraries, with default parameters for single-end, […]

PMCID: 5553385
PMID: 28810711
DOI: 10.1093/gbe/evx143

[…] last accessed july 28, 2017) to remove adapters and sequences with low phred-scores (cutoff: ≥20)., for assembling whole transcriptomes, we used two different strategies: a de novo approach using binpacker version 1.0 () and a reference based assembly using stringtie version 1.3.0 () with two different alignment programs: hisat2 version 2.0.4 () and subjunc version 1.22.3 (). both hisat2 […]

PMCID: 5481918
PMID: 28645248
DOI: 10.1186/s12864-017-3840-1

[…] to quality trimming (using a threshold of phred <2, as per []) and adapter removal using skewer version 0.1.127 []. these reads were then assembled in the de novo transcriptome assembler binpacker version 1.0 []. we also reduced sequence redundancy to improve the assembly using the sequence clustering software cd-hit-est version 4.6 [, ]. we further optimized the assembly […]

PMCID: 5394691
PMID: 28417958
DOI: 10.1038/srep45125

[…] were error corrected using rcorrector version 1.0.2. adapters, as well as bases with a phred score <2 were trimmed using skewer 0.2.2, and assembly was carried out using trinity version 2.2.0, binpacker version 1.0, and shannon version 0.0.2, after which the resultant transcriptomes were merged using the software package transfuse version 0.5.0 (https://github.com/cboursnell/transfuse). […]


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BinPacker institution(s)
School of Mathematics, Shandong University, Jinan, China; High Performance Computing Center, University of Arkansas, Fayetteville, AR, USA; Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, USA; Department of Computer Science, Arkansas State University, Jonesboro, AR, USA
BinPacker funding source(s)
This work was funded by National Natural Science Foundation of China with codes 61432010, 61272016 and 31571354; National Science Foundation with number 1553680; National Center for Research Resources with number P20RR016460; and National Institute of General Medical Sciences with number P20GM103429.

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