Genboree Workbench statistics

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Associated diseases

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Genboree Workbench specifications


Unique identifier OMICS_01142
Name Genboree Workbench
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Parallelization MapReduce
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes


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Publications for Genboree Workbench

Genboree Workbench in publications

PMCID: 5913337
PMID: 29686252
DOI: 10.1038/s41598-018-24765-6

[…] rna sequencing was performed on an ion proton system using the ion pi hi-q chef kit (life technologies, usa)., detailed procedures for this analysis using the excerpt tool available on the genboree workbench [] were previously published. after alignment to endogenous sequences and removal of all contaminants with endogenous sequences, the software aligned […]

PMCID: 5424369
PMID: 28486933
DOI: 10.1186/s12866-017-1022-6

[…] this toolset has integrated open source tools for 16s rrna gene analyses, such as the ribosomal database project (rdp) classifier [] and qiime (quantitative insights into microbial ecology) []., the genboree workbench was used to upload the sequencing sff-files for each sample together with the associated sample metadata. individual sequencing files were passed through a quality filtering […]

PMCID: 4977539
PMID: 27503761
DOI: 10.1038/srep31175

[…] construction of the nebnext small rna libraries, followed by the hiseq 2000 rna-seq. read mapping to the hg19 version of human genome was performed using the excerpt small rna-seq pipeline v2.2.8 of genboree workbench with default parameters. on average, 13.6% and 21.7% reads from the “pellet rna” and “supernatant rna” fractions, respectively, were mapped to the human genome, suggesting […]

PMCID: 4945050
PMID: 27415797
DOI: 10.1371/journal.pone.0155888

[…] pearson correlation distance. additional sequencing analysis was also performed using the mirna analytical workflow cap-mirseq, developed at the mayo clinic bioinformatics core, and by using the genboree workbench excerpt pipeline from the nih extracellular rna communications consortium.[] sequencing data will be made available at the exrna atlas.[] mirna target analysis was performed using […]

PMCID: 4887520
PMID: 27247029
DOI: 10.3402/jev.v5.31552

[…] and exrna metadata tracking tools. data analysis tools such as the excerpt small rna-seq pipeline, rseqtools long rna-seq pipeline, pathway finder and target interaction finder are available in the genboree workbench. the excerpt pipeline generates a variety of sample-level quality control metrics, produces abundance estimates for various small rna species and makes available detailed alignment […]

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