EP_metagenomic specifications

Unique identifier:
Command line interface
Input data:
It requires the following input parameters: (1) a prefix for the output files (no whitespaces in prefix). A directory with the same name will be created in which the output files are saved; (2) the number of cores that should be used for the computations; (3) a file with the aligned (!) reads and extended MD tag. Only aligned reads should be included; (4) a file in sam format with the aligned (!) reads. Only aligned reads should be included; and (5) the maximum read length (e.g. the original length of the sequenced reads).
Operating system:
Computer skills:
Software type:
Restrictions to use:
Biological technology:
Programming languages:
Perl, R, Shell (Bash)


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EP_metagenomic support


  • Melanie Schirmer <>


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The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard T.H. Chan School of Public Health, Boston, MA, USA; University of Liverpool, Centre for Genomic Research, Liverpool, UK; University of Glasgow, School of Engineering, Glasgow, UK; University of Warwick, Warwick Medical School, Coventry, UK

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