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Protocols

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

Versioning


No version available

Maintainer


This tool is not maintained anymore.

Publication for JAGUC

JAGUC citations

 (6)
library_books

Acidotolerant Bacteria and Fungi as a Sink of Methanol Derived Carbon in a Deciduous Forest Soil

2017
Front Microbiol
PMCID: 5523551
PMID: 28790984
DOI: 10.3389/fmicb.2017.01361

[…] potential 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 simila […]

library_books

Associative nitrogen fixation in nodules of the conifer Lepidothamnus fonkii (Podocarpaceae) inhabiting ombrotrophic bogs in southern Patagonia

2016
Sci Rep
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 and are […]

library_books

The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates

2016
Sci Rep
PMCID: 5025661
PMID: 27633177
DOI: 10.1038/srep33555

[…] d 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 to reduce […]

call_split

High diversity of protistan plankton communities in remote high mountain lakes in the European Alps and the Himalayan mountains

2015
PMCID: 4399440
PMID: 25764458
DOI: 10.1093/femsec/fiv010
call_split See protocol

[…] in 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 - […]

call_split

Evidence for isolated evolution of deep sea ciliate communities through geological separation and environmental selection

2013
BMC Microbiol
PMCID: 3707832
PMID: 23834625
DOI: 10.1186/1471-2180-13-150
call_split See protocol

[…] s. 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 calibrati […]

call_split

Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces

2013
PLoS One
PMCID: 3572030
PMID: 23418556
DOI: 10.1371/journal.pone.0056335
call_split See protocol

[…] t method of all-to-all pair-wise comparisons via the pick_otus.py command.The QIIME taxonomy classification pipeline was not able to accurately classify the majority of eukaryotic OTUs. Thus, we used Jaguc, a program developed specifically for classification of eukaryotic rRNA sequence data, to classify our sequence reads . 90% of eukaryotic OTUs were classified to genus using this approach. OTU t […]


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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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