PMDtools protocols

View PMDtools computational protocol

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PMDtools specifications

Information


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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Documentation


Maintainer


  • person_outline Pontus Skoglund <>

Publication for PMDtools

PMDtools in pipeline

2017
PMCID: 5724682
PMID: 28884802
DOI: 10.1002/ajpa.23308

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


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PMDtools in publications

 (12)
PMCID: 5867856
PMID: 29494531
DOI: 10.3390/genes9030135

[…] calculation, rx and ry were also determined using only reads showing signs of damage, as these reads are unlikely to have originated from modern contaminants []. read filtering was performed using pmdtools (v0.50; []) with a threshold of three, as recommended by the author of the program., sequencing results for all four post-capture library runs are presented in . the size distributions […]

PMCID: 5499742
PMID: 28486705
DOI: 10.1093/nar/gkx361

[…] generated using a proofreading platinum high fidelity taq polymerase (). we mapped all saqqaq read files from the sequence read archive (n = 218) to a human mitochondrial genome (eu256375.1), used pmdtools () to rapidly generate misincorporation plots and visually inspected each for elevated 5΄ c-to-t mismatch. this approach yielded two libraries apparently produced using a proofreading […]

PMCID: 5321759
PMID: 28221340
DOI: 10.1038/ncomms14115

[…] of misalignment and were manually corrected based on visualization of the sequence reads., to verify support for the consensus haplotype among only reads with deaminated cytosine residues, we used pmdtools to generate bam files from fragments having a minimum post-mortem degradation (pmd) score of 3, retaining ∼15–43% of reads per alignment. we re-ran mapdamage to generate new lambda values, […]

PMCID: 5287702
PMID: 28164156
DOI: 10.1126/sciadv.1601877

[…] devil’s gate (oxcal version 4.2.4)., fig. s2. damage patterns for samples from devil’s gate., fig. s3. sequence length distribution for samples from devil’s gate., fig. s4. outgroup f3 statistics on pmdtools-filtered data., fig. s5. pca on all snps using the worldwide panel., fig. s6. pca on transversion snps using the worldwide panel., fig. s7. pca on all snps using the regional panel., fig. […]

PMCID: 5384568
PMID: 28392981
DOI: 10.7717/peerj.3126

[…] a reference genome allows researchers to easily eliminate non-endogenous dna and identify erroneous base incorporations. these errors can be identified after the mapping, e.g., by mapdamage () or pmdtools (), and used to verify that the sequenced fragments stem from ancient specimen., the reference-based mapping approaches cannot detect large insertions or other genomic architectural […]


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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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