JR-Assembler statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Genome assembly chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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

Versioning


Add your version

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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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.

JR-Assembler reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review JR-Assembler