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

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Publication for Genometa

Genometa in publications

 (5)
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 […]

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 […]

PMCID: 4726098
PMID: 26778510
DOI: 10.1038/srep19233

[…] in some cases, also shed light on the functional composition of the community. these tools can broadly be separated in two groups - those using all available sequences for each data set (e.g. clark, genometa, gottcha, kraken, lmat, megan, mg-rast, the one codex webserver, taxator-tk) and those focusing on a set of marker genes (e.g metaphlan, metaphyler , motu, qiime)., a previous benchmark used […]

PMCID: 4059276
PMID: 24982662
DOI: 10.3389/fpls.2014.00209

[…] 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 […]

PMCID: 4222586
PMID: 24267292
DOI: 10.1186/1471-2121-14-51

[…] user guide (part no. 4460960), 5500 solid™ fragment library core kit (part no. 4464412) and ez bead™ e20 system consumables (part no. 4453094)). subsequent analysis was performed with the program genometa []., after three times washing, mouse embryonic fibroblasts or hepa1-6 cells were lysed with lysis buffer (10 mm tris, 150 mm nacl, 1 mm pmsf, 0.5% np40, protease inhibitor cocktail, […]


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

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