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mapDamage specifications

Information


Unique identifier OMICS_02099
Name mapDamage
Alternative name mapDamage2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Version 2.0
Stability Stable
Requirements
gam, python, bedtools, pysam, cython, ggplot2 0.9.2
Maintained Yes

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Publications for mapDamage

mapDamage citations

 (61)
library_books

Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans

2018
Nat Commun
PMCID: 5931558
PMID: 29717136
DOI: 10.1038/s41467-018-03857-x

[…] -i $IN -o $OUTwhere $IN is the input BAM file and $OUT is the output BAM file.To authenticate aDNA data sets, we evaluated the presence of postmortem DNA damage signatures from read alignments using mapDamage v2.0.6 with default parameters and the following command:mapDamage -v -i $BAM -r $REF -l 100 -d $PREFIXwhere $BAM is the input BAM file containing only merged reads, $REF is the reference FA […]

library_books

Maternal DNA lineages at the gate of Europe in the 10th century AD

2018
PLoS One
PMCID: 5851556
PMID: 29538439
DOI: 10.1371/journal.pone.0193578

[…] a probabilistic iterative approach, Schmutzi [], was used to call the endogenous consensus sequences and to estimate the contamination levels. Misincorporation patterns were tracked and quantified by mapDamage 2.0 []. The latter one was also executed for the reconstruction of endogenous mitochondrial genomes. Classification of complete mtDNA sequences according to haplogroup nomenclature was achie […]

library_books

Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool

2018
Genes
PMCID: 5867878
PMID: 29533977
DOI: 10.3390/genes9030157

[…] istribution can be specified by the user. The desired patterns of nucleotide mis-incorporation in the simulated read set can be inferred from preliminary data exploration using the commonly-used tool mapDamage [] or alternatively specified by the user. Simulated endogenous reads can be subjected to random base substitutions, which would reflect genetic distance between the target sequence and refe […]

library_books

Biological Sexing of a 4000 Year Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens

2018
Genes
PMCID: 5867856
PMID: 29494531
DOI: 10.3390/genes9030135

[…] . Data observed in the reagent blanks and negative controls were mapped and analyzed using the same parameters.To assess data authenticity, C-T and G-A errors due to deamination were quantified using MapDamage 2.0 []. Modern DNA contamination was estimated using ContamMix [] and by evaluating the number of human sequences observed in the extraction (RB) and library preparation control (NC) samples […]

call_split

Ancient mitogenomes of Phoenicians from Sardinia and Lebanon: A story of settlement, integration, and female mobility

2018
PLoS One
PMCID: 5761892
PMID: 29320542
DOI: 10.1371/journal.pone.0190169
call_split See protocol

[…] RS.PCR duplicates were marked and removed from unmerged reads using Picard tools 1.92 (http://broadinstitute.github.io/picard/), and from merged reads using a python script developed by Fu et al. []. MapDamage (v2.0.2–9) [] was used to identify characteristic aDNA damage patterns, with the ‘-rescale’ option to lower the quality score of likely damaged sites. Thiamines (T) found at the 5’end of a r […]

call_split

The paradox of HBV evolution as revealed from a 16th century mummy

2018
PLoS Pathog
PMCID: 5754119
PMID: 29300782
DOI: 10.1371/journal.ppat.1006750
call_split See protocol

[…] sitions (https://bitbucket.org/ustenzel/biohazard). Reads shorter than 30 base pairs and with mapping quality less than 30 were removed using Samtools []. The resulting BAM files were processed using mapDamage 2.0 on default settings with plotting and statistical estimation []. Haplogrep v2.1.0 [] using PhyloTree Build 17 [] was used to identify the haplogroup of the mtDNA as U5a1b. The complete g […]

Citations

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mapDamage institution(s)
Centre for Geogenetics, Natural History Museum of Denmark, Copenhagen University, Denmark
mapDamage funding source(s)
Danish Council for Independent Research; Natural Sciences (FNU); Danish National Research Foundation (Danmarks Grundforskningsfond)

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