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Protocols

RITA specifications

Information


Unique identifier OMICS_10783
Name RITA
Alternative name Rapid Identification of Taxonomic Assignments
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.0.1
Stability Stable
Requirements
BLAST+
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Rob Beiko

Information


Unique identifier OMICS_10783
Name RITA
Alternative name Rapid Identification of Taxonomic Assignments
Interface Web user interface
Restrictions to use None
Programming languages Python
Computer skills Basic
Version 1.0.1
Stability Stable
Maintained Yes

Maintainer


  • person_outline Rob Beiko

Publications for Rapid Identification of Taxonomic Assignments

RITA citations

 (7)
library_books

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

2015
BMC Bioinformatics
PMCID: 4634789
PMID: 26537885
DOI: 10.1186/s12859-015-0788-5

[…] rized microbiomes (such as in water versus human feces) the use of such conservative methods could be entirely appropriate. The pipeline idea of combining methods is integrated into some methods like RITA, which first identifies a highest-confidence set of predictions, then subjects the sequences not yet classified to a series of downstream classification steps. CARMA3 performs well in both the no […]

library_books

Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities

2015
BMC Genomics
PMCID: 4502571
PMID: 26173980
DOI: 10.1186/s12864-015-1752-5

[…] Class-level taxonomic classification of contigs was done using RITA []. RITA uses a reference database to assign a taxonomic classification to sequence data using both homology and nucleotide composition. We used RITA v1.0.1 with a reference data set of over 2986 […]

call_split

Microbial shifts in the aging mouse gut

2014
Microbiome
PMCID: 4269096
PMID: 25520805
DOI: 10.1186/s40168-014-0050-9
call_split See protocol

[…] ounts were subjected to taxonomic analysis. To determine and compare the taxonomic characterization of these particular functions, metagenomic reads annotated with these functions were analyzed using RITA []. Briefly, RITA uses a reference database of sequenced and draft genomes to list the annotated proteins for each genome and construct compositional models of each genome. RITA uses a combinatio […]

library_books

Evaluation of a Hybrid Approach Using UBLAST and BLASTX for Metagenomic Sequences Annotation of Specific Functional Genes

2014
PLoS One
PMCID: 4210140
PMID: 25347677
DOI: 10.1371/journal.pone.0110947

[…] especially for large datasets.A previous study proposed a hybrid approach for taxonomic annotation . It used multiple alignment processes (UBLAST and BLASTX) to accelerate homology search and achieve rapid identification of taxonomic assignments for metagenomic data. In the present study, we first compared the time consumed and annotation results of two ultra-fast alignment tools, i.e. RAPSearch2 […]

library_books

New Insights into Dehalococcoides mccartyi Metabolism from a Reconstructed Metabolic Network Based Systems Level Analysis of D. mccartyi Transcriptomes

2014
PLoS One
PMCID: 3986231
PMID: 24733489
DOI: 10.1371/journal.pone.0094808

[…] ng “nucmer” program from the MUMmer package . The contigs with identified homology to these reference genomes were parsed out and utilized for the initial attempts at D. mccartyi genome closure. Once RITA classifications (http://kiwi.cs.dal.ca/Software/RITA) were available for the KB-1 contigs and singletons, additional D. mccartyi sequences were added to the draft genome. The initial D. mccartyi […]

library_books

Analytical Tools and Databases for Metagenomics in the Next Generation Sequencing Era

2013
PMCID: 3794082
PMID: 24124405
DOI: 10.5808/GI.2013.11.3.102

[…] ed approaches together to gain accuracy and discard fewer reads. PhymmBL linearly combines the BLASTN score and Phymm score and thereby gains more power to discriminate between similar BLAST hits []. RITA also combines a BLAST search with a composition-based NBC; however, unlike PhymmBL, RITA puts more weight on the BLAST result []. Both approaches are reported to perform well, even with short rea […]

Citations

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RITA institution(s)
Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
RITA funding source(s)
Natural Sciences and Engineering Research Council of Canada; the Killam Trusts; Genome Atlantic; the Canada Foundation for Innovation; the Canada Research Chairs program; the Government of Canada through Genome Canada and the Ontario Genomics Institute [2009-OGI-ABC-1405]

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