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Genometa specifications

Information


Unique identifier OMICS_02175
Name Genometa
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for Genometa

Genometa citations

 (5)
library_books

TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms

2017
BMC Genomics
PMCID: 5644092
PMID: 29037173
DOI: 10.1186/s12864-017-4168-6

[…] for the taxonomic classification of metagenomic reads using known bacterial genomes. GOTTCHA [] is a taxonomic profiler that uses non-redundant signature databases for prokaryotic and viral genomes. Genometa [] is a Java program to identify bacterial species and gene content from high-throughput datasets. MetaPhyler [] estimates bacterial composition from metagenomic samples.Others use a subset o […]

library_books

Filtration and Normalization of Sequencing Read Data in Whole Metagenome Shotgun Samples

2016
PLoS One
PMCID: 5070866
PMID: 27760173
DOI: 10.1371/journal.pone.0165015

[…] the methods implemented in these tools failed to address the GC bias problem and only a few of them address the issues of length difference of the reference sequences [,,]. To our knowledge only the Genometa pipeline [] currently implements a check for potential false positive hits due to clustered genomic island reads, without addressing the first two problems (GC bias and length difference of t […]

library_books

Current Technological Improvements in Enzymes toward Their Biotechnological Applications

2016
Front Microbiol
PMCID: 4909775
PMID: 27379087
DOI: 10.3389/fmicb.2016.00965

[…] recruitment, in which, reads are aligned to nearly identical genome sequences to produce metagenomic coverage estimates of the genome. There are several tools that help to map the reads viz. MOSAIK, Genometa, SOAP, BWA, CLC, RefCov. (3) Assembly reads that posses nearly identical sequences at their ends are linked to form contig or complete genome. Each successive sequencing project adds to the p […]

library_books

An evaluation of the accuracy and speed of metagenome analysis tools

2016
Sci Rep
PMCID: 4726098
PMID: 26778510
DOI: 10.1038/srep19233

[…] , and the functional annotations are added using InterProScan against a set of databases (including Gene3D, Pfam and PROSITE), and each predicted gene is associated with a set of Gene Ontology terms. Genometa: Genometa is a GUI (Graphical User Interface) program building on the Integrated Genome Browser (IGB) and using the Bowtie mapper. Reads are mapped to a custom genome database and results can […]

library_books

An introduction to the analysis of shotgun metagenomic data

2014
Front Plant Sci
PMCID: 4059276
PMID: 24982662
DOI: 10.3389/fpls.2014.00209

[…] the abundance of metabolic pathways (; see Gene Prediction). There are currently few tools that will handle both the mapping of reads to a database of genomes and the calculation of genome abundance. Genometa () is one such tool and provides a graphical user interface. () evaluated the performance of several commonly used short read mapping algorithms (e.g., SOAP, BWA, CLC) in fragment recruitment […]

Citations

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Genometa institution(s)
Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Lower Saxony, Germany

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