PMDtools pipeline

PMDtools specifications


Unique identifier OMICS_08848
Name PMDtools
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data PMDtools takes SAM-formatted input, and requires an MD tag with alignment information.
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.50
Stability Stable
Maintained Yes


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  • person_outline Pontus Skoglund <>

Publication for PMDtools

PMDtools IN pipeline

PMCID: 5724682
PMID: 28884802
DOI: 10.1002/ajpa.23308

[…] checked for presence of 3′ and 5′ degradation patterns characteristic of ancient dna (briggs et al., 2007, brotherton et al., 2007, sawyer, krause, guschanski, savolainen, & pääbo, 2012) using pmdtools (skoglund et al., 2014). molecular sex assignment was estimated based on the ratio of sequences aligning to the two sex chromosomes, x and y (skoglund, storå, götherström, & jakobsson, […]

PMDtools institution(s)
Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences Siberian Branch, Novosibirsk, Russia; Institute for Archaeological Sciences, University of Tuebingen, Tuebingen, Germany

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