Jellyfish pipeline

Jellyfish specifications

Information


Unique identifier OMICS_01056
Name Jellyfish
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Additional information


http://www.cbcb.umd.edu/software/jellyfish/

Publication for Jellyfish

Jellyfish IN pipelines

 (24)
2018
PMCID: 5905561
PMID: 29444297
DOI: 10.1093/gigascience/giy006

[…] a total of 10.6 and 11.3 gb of high-quality data (approximately 39.3 and 36.8x) were retained for genome assembly (table 1)., first, we performed 17-mer analysis to estimate the genome size using jellyfish (jellyfish, rrid:scr_005491) [25] and all the high-quality sequences (10.6 and 11.3 gb). the estimated genome size was around 270 mb for h. cichorii and 308 mb for h. phaleratus (table 2). […]

2018
PMCID: 5905561
PMID: 29444297
DOI: 10.1093/gigascience/giy006

[…] of 10.6 and 11.3 gb of high-quality data (approximately 39.3 and 36.8x) were retained for genome assembly (table 1)., first, we performed 17-mer analysis to estimate the genome size using jellyfish (jellyfish, rrid:scr_005491) [25] and all the high-quality sequences (10.6 and 11.3 gb). the estimated genome size was around 270 mb for h. cichorii and 308 mb for h. phaleratus (table 2). moreover, […]

2017
PMCID: 5244389
PMID: 28102365
DOI: 10.1038/srep40712

[…] 4,300 genomes were obtained. viroid and satellite data were excluded from the dataset, and then 3,905 genomes remained for this research. all genome data were converted to k-mer feature counts with jellyfish software43. the dataset was also divided into four subsets by 25%, 50%, and 75% quantile cut-offs of genomic size in order to explore how optimal feature lengths vary by genomic size., […]

2017
PMCID: 5293829
PMID: 28223970
DOI: 10.3389/fmicb.2017.00156

[…] that had in their 11th position either the donor or recipient base. we challenged this reference snp library against a 20mer database created from the fastq of the post-mating mixture using jellyfish software (marçais and kingsford, 2011). from the counts of the donor and recipient 20mers at each base, we were able to (1) map recombinant boundaries and (2) ascertain the extent of mixed […]

2017
PMCID: 5301235
PMID: 28186206
DOI: 10.1038/srep42444

[…] 280 dh lines of the ibm syn10 population used to build an ultra-high density genetic map10 were trimmed with trimmomatic (version 3.2)59. remaining clean reads were subjected to k-mer counting with jellyfish. the k-mer size is 25 nt. the abundance of each hakmer with differential abundance in b73 and mo17 was determined in each dh line. the total counts (c) of a million of randomly selected b73 […]

Jellyfish institution(s)
Program in Applied Mathematics, Statistics and Scientific Computation, University of Maryland, College Park, MD, USA; Department of Computer Science and Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA
Jellyfish funding source(s)
National Science Foundation (grants EF-0849899 and IIS-0812111); National Institutes of Health (grant 1R21AI085376); National Science Foundation (grant DMS-0616585); National Institutes of Health (grant 1R01HG0294501)

Jellyfish review

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Calvi Caswara

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Desktop
fast tool, easy to handle and install