MicrobeCensus protocols

MicrobeCensus specifications

Information


Unique identifier OMICS_07840
Name MicrobeCensus
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements Numpy, BioPython
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Katherine S. Pollard <>

Publication for MicrobeCensus

MicrobeCensus IN pipelines

 (4)
2017
PMCID: 5363007
PMID: 28330508
DOI: 10.1186/s40168-017-0244-z

[…] (afl) or the average length of the matched genes within a gene familyaverage genome size (ags) or the estimated average genome length based on single-copy universal marker genes (estimated using microbecensus: [36] http://github.com/snayfach/microbecensus). , average family length (afl) or the average length of the matched genes within a gene family, average genome size (ags) […]

2017
PMCID: 5363007
PMID: 28330508
DOI: 10.1186/s40168-017-0244-z

[…] genes within a gene familyaverage genome size (ags) or the estimated average genome length based on single-copy universal marker genes (estimated using microbecensus: [36] http://github.com/snayfach/microbecensus). , average family length (afl) or the average length of the matched genes within a gene family, average genome size (ags) or the estimated average genome length based on single-copy […]

2017
PMCID: 5363007
PMID: 28330508
DOI: 10.1186/s40168-017-0244-z

[…] (afl) or the average length of the matched genes within a gene family, average genome size (ags) or the estimated average genome length based on single-copy universal marker genes (estimated using microbecensus: [36] http://github.com/snayfach/microbecensus)., normalization for these two factors yielded abundance values in units of rpkg or reads per kilobase of genome equivalents [36]., […]

2017
PMCID: 5363007
PMID: 28330508
DOI: 10.1186/s40168-017-0244-z

[…] within a gene family, average genome size (ags) or the estimated average genome length based on single-copy universal marker genes (estimated using microbecensus: [36] http://github.com/snayfach/microbecensus)., normalization for these two factors yielded abundance values in units of rpkg or reads per kilobase of genome equivalents [36]., these rpkg abundance values were strictly positive […]

MicrobeCensus institution(s)
Integrative Program in Quantitative Biology, University of California, San Francisco, CA, USA

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