Apollo pipeline

Apollo specifications

Information


Unique identifier OMICS_11761
Name Apollo
Alternative name WebApollo
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Javascript, Perl
Computer skills Advanced
Version 2.0.2
Stability Stable
Source code URL https://codeload.github.com/GMOD/Apollo/zip/master
Maintained Yes

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Maintainer


  • person_outline Eduardo Lee <>

Publications for Apollo

Apollo IN pipelines

 (3)
2018
PMCID: 5902842
PMID: 29661190
DOI: 10.1186/s12864-018-4656-3

[…] a second a. chinensis genotype, red5, with higher homozygosity than ‘hongyang’. this information was combined with est sequencing results [25] and rna-seq data and made available to annotators via webapollo to facilitate manual annotation of the new genome. the whole genome was manually annotated, resulting in what we believe to be a considerable improvement in allocating previously […]

2016
PMCID: 5034548
PMID: 27659211
DOI: 10.1186/s13059-016-1049-2

[…] that produced hits (<1e–10) were used to query, using blastx, local protein databases of the d. melanogaster and m. domestica obps and ors. the gene models were modified, where necessary, in webapollo. the medfly genes were named using a numerical system, with genes on the same scaffold numbered sequentially. however, for the obps, the sequential numbering system was modified to permit […]

2011
PMCID: 3037005
PMID: 21304167
DOI: 10.1128/mBio.00342-10

[…] we identified and annotated 6,565 potential open reading frames (orfs; excluding pseudogenes). these orfs were identified and annotated using pegasys (28), which includes the atlas database (29) and apollo (30, 31) for the curators to interpret gene models and make decisions based on the evidence presented to them. the evidence was built from gene prediction models, blastp (32) […]

Apollo institution(s)
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Division of Animal Sciences, University of Missouri, Columbia, MO, USA; Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA; Ontario Institute of Cancer Research, MaRS Centre, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
Apollo funding source(s)
This work was supported by the National Institutes of Health (5R01GM080203) by the National Institute of General Medical Sciences; by the National Human Genome Research Institute (5R01HG004483), and by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy ( DE-AC02-05CH11231).

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