JAGUC protocols

View JAGUC computational protocol

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JAGUC specifications

Information


Unique identifier OMICS_25038
Name JAGUC
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Requirements
JRE, MySQL, megablast
Maintained No

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This tool is not maintained anymore.

Publication for JAGUC

JAGUC in pipeline

2015
PMCID: 4399440
PMID: 25764458
DOI: 10.1093/femsec/fiv010

[…] edgar et al. (). for our pyro-amplicons, a value of 64 was used. for taxonomic assignments, one representative sequence (longest) from each otu was extracted and analyzed with the software package jaguc (nebel et al., ) and genbank´s nr nucleotide database release 187 as reference database. jaguc employs blastn searches, with algorithm parameters adjusted for short reads (-m 7 -r 5 -q -4 -g 8 […]


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JAGUC in publications

 (6)
PMCID: 5523551
PMID: 28790984
DOI: 10.3389/fmicb.2017.01361

[…] 16s rrna chimeric sequences were sorted out using the uchime algorithm implemented in usearch and the latest rdp gold database for high-quality 16s rrna gene reference sequences (; ). using jaguc v2.1, the sequences were clustered into operational taxonomic units (otus) applying the upgma model (). the otus of 16s rrna were clustered at the family level using 90.1% as the pairwise […]

PMCID: 5157042
PMID: 27976730
DOI: 10.1038/srep39072

[…] peat cdna). per gene library, plasmids were extracted from 96 clones, and inserts were sanger sequenced (4 gene libraries x 96) at lgc genomics (berlin, germany). nifh sequences were clustered with jaguc2 and otus were called at 97% sequence similarity. cluster representatives were phylogenetically affiliated with blastx. 264 nifh genes and transcripts grouping into 2αtus were recovered […]

PMCID: 5025661
PMID: 27633177
DOI: 10.1038/srep33555

[…] in oikonomou et al.. for final taxonomic assignment of the otus the representative read (longest) of each otu was subjected to blast analyses against genbank’s nr nucleotide database release 200 in jaguc. jaguc employs blastn searches with algorithm parameters adjusted for short reads (-m 7 -r 5 -q -4 -g 8 -e 6 -b 50). singletons and doubletons otus were excluded from the final dataset […]

PMCID: 4399440
PMID: 25764458
DOI: 10.1093/femsec/fiv010

[…] edgar et al. (). for our pyro-amplicons, a value of 64 was used. for taxonomic assignments, one representative sequence (longest) from each otu was extracted and analyzed with the software package jaguc (nebel et al., ) and genbank´s nr nucleotide database release 187 as reference database. jaguc employs blastn searches, with algorithm parameters adjusted for short reads (-m 7 -r 5 -q -4 -g 8 […]

PMCID: 3707832
PMID: 23834625
DOI: 10.1186/1471-2180-13-150

[…] the number of amplicons obtained after sequencing ranged between 33,634 (thetis brine) and 80,650 (urania interface) sequences., for sequence data quality control and processing, we used the program jaguc []. all tags that met any of the following conditions were considered as “low quality” and removed from further analyses: sequences <200 nucleotides, sequences containing an inaccurate […]


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JAGUC institution(s)
Computer Science Department, University of Kaiserslautern, Kaiserslautern, Germany; Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany

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