JR-Assembler specifications

Information


Unique identifier OMICS_00018
Name JR-Assembler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Arthur Chun-Chieh <>

Publication for JR-Assembler

JR-Assembler in publications

 (6)
PMCID: 5819677
PMID: 29463212
DOI: 10.1186/s12864-018-4539-7

[…] initial assembly of the a. limnaeus genome at a sequencing coverage of 94x. this allpaths-lg assembly produced 141,049 contigs longer than 1000 bp, and within these contigs 650 mbp was assembled. jr-assembler assembled 370,267 contigs (> 500 bp) with an n50 of 1.3 kbp and a total assembled length of 433 mbp. after merging the two assembles with a graph accordance assembly program [], […]

PMCID: 5062080
PMID: 27734962
DOI: 10.1038/srep35076

[…] script to remove linkers and pair up the corresponding reads. the slr reads were generated via basespace module (illumina) and used as given., we ran the assembly tools allpaths-lg, masurca, and jr-assembler on our pe reads with mp reads set as jump reads for scaffolding. we found allpaths-lg to be the most favorable as far as number of scaffolds and total genome length are concerned. […]

PMCID: 4730604
PMID: 26823972
DOI: 10.1186/s13742-016-0108-7

[…] heterozygosity, we used a hybrid assembly approach to assemble the genome of race 0 (fig. ). we also compared the performance of different assemblers including velvet (v1.2.09) [], abyss (v3.81) [], jr-assembler (v1.0.3) [], euler-sr (v1.1.2) [], spades (v3.0.0) [], soapdenovo2 (r240) [], celera assembler (v8.0) [] and minimus2 (v 3.1) [] on p. nicotianae race 0. comparison showed […]

PMCID: 4607514
PMID: 26384038
DOI: 10.1093/gbe/evv154

[…] velvet (v1.2.10, k = 55) (), abyss (v1.3.4, k = 45) (), spades mainly implemented for single-cell data (v2.5.1, k = 43,55,65) ()—all de bruijn graph based ()—and the seed-and-extend approach based jr-assembler (v1.0.3, default parameters) (). the resulting contigs (>1,000 bp) were merged and clustered for sequence similarities using cd-hit-est (v4.6, -c 0.95) () to reduce redundancy. […]

PMCID: 4512556
PMID: 25995208
DOI: 10.1534/genetics.115.175950

[…] information, figure s1; table s1). this process allowed extension of sequence into regions of high divergence, closed large deletions, and built sequence into insertions ( and ). we used the jr-assembler () to create de novo assemblies of the same sequence reads, assessed their quality using the program reapr (), breaking contigs as needed, and aligned the resultant contigs […]


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JR-Assembler institution(s)
Institute of Information Science, Academia Sinica, Taipei, Taiwan, China; Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, China; Research Center for Information Technology Innovation, Academia Sinica, Taipei, Taiwan, China; Department of Computer Science and Information Engineering, National Taiwan Normal University, Taipei, Taiwan, China; Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan, Taiwan, China; Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA
JR-Assembler funding source(s)
Supported by Academia Sinica and by National Science Council (Taiwan) Grants NSC99-2218-E-006-012, NSC99-3113- B-001-001, NSC 99-2321-B-001-041-MY2, and NSC 99-2621-B-001-003-MY3.

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