TaxMapper specifications

Information


Unique identifier OMICS_20345
Name TaxMapper
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format CSV
Output format PDF
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Requirements
numpy, pandas, matplotlib, deepdish, rapsearch
Maintained Yes

Download


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Versioning


No version available

Maintainers


  • person_outline Sven Rahmann
  • person_outline Daniela Beisser
  • person_outline Nadine Graupner
  • person_outline Lars Grossmann
  • person_outline Jens Boenigk

Publication for TaxMapper

TaxMapper citation

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

[…] also be an option to remove rRNA from the samples and keep prokaryotic sequences, but from our experience this may lead to a high abundance of prokaryotic sequences with few eukaryotic reads. To use TaxMapper on such samples, we recommend to first filter out prokaryotic reads and then use TaxMapper on the remaining reads. Without splitting the dataset, the analysis will be more time-demanding and […]

TaxMapper institution(s)
Biodiversity, University of Duisburg-Essen, Essen, Germany; Genome Informatics, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
TaxMapper funding source(s)
Supported by the Deutsche Forschungsgemeinschaft (DFG) through the Priority Programme DynaTrait (SPP 1704), grants RA 1898/1-1 and BO 3245/14-1.

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