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JR-Assembler specifications


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


No version available



  • person_outline Arthur Chun-Chieh

Publication for JR-Assembler

JR-Assembler citations


The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development

BMC Genomics
PMCID: 5819677
PMID: 29463212
DOI: 10.1186/s12864-018-4539-7

[…] d to pass the Illumina purity filter were retained in the read pool for de novo assembly. In a separate assembly, the fragment reads were error corrected using Allpaths-LG and de novo assembled using JR-assembler, an assembler that is based on read overlap to extend contigs []. Prior to assembly with JR-assembler, reads were trimmed to 90 bp and filtered using the included mdust algorithm. Contigs […]


Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance

Sci Rep
PMCID: 5062080
PMID: 27734962
DOI: 10.1038/srep35076

[…] 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. After t […]


Comparative Genomics of Pathogens Causing Brown Spot Disease of Tobacco: Alternaria longipes and Alternaria alternata

PLoS One
PMCID: 4861331
PMID: 27159564
DOI: 10.1371/journal.pone.0155258

[…] as calculated and plotted. The genome size G = K_num/Peak_depth, where the K_num is the total number of 17-mer, and Peak_depth is the expected value of 17-mer depth.We assembled the short reads using JR-Assembler []–an extension-based de novo assembler. It runs in five steps: raw read processing, seed selection, seed extension, repeat detection, and contig merging by SSAKE based Scaffolding of Pre […]


Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856

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

[…] define their end points. As a result, they had not been removed in our iterative alignment and correction procedure. To resolve these regions, we exploited a new whole-genome assembly algorithm, the JR-Assembler (), which compares favorably to current assemblers in terms of quality, efficiency, and memory. We used the JR-Assembler to create a de novo assembly of the CB4856 genome. To reduce the n […]


America's red gold: multiple lineages of cultivated cochineal in Mexico

Ecol Evol
PMCID: 4328766
PMID: 25691985
DOI: 10.1002/ece3.1398
call_split See protocol

[…] A draft Dactylopius coccus genome assembly was constructed using JR-Assembler 1.02 (Chu et al. ; Table). The final assembly was 18.6 Mbp long with an N50 of 378,999 bp (Table). The quality-controlled merged sequence reads were aligned against the D. coccus assembly […]


A field guide to whole genome sequencing, assembly and annotation

Evol Appl
PMCID: 4231593
PMID: 25553065
DOI: 10.1111/eva.12178

[…] eads can be broadly divided into two classes: extension-based methods and De Bruijn (or Eulerian) graph algorithms (Nagarajan and Pop ). Extension-based assemblers, such as SSAKE (Warren et al. ) and JR-Assembler (Chu et al. ) are usually computationally very efficient (in terms of both memory requirements and computational time), but are highly sensitive to sequencing errors, repeat regions and h […]


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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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