mapDamage specifications

Information


Unique identifier OMICS_02099
Name mapDamage
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
Maintained Yes

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mapDamage articles

mapDamage citations

 (2)
2017
PMCID: 5335606

[…] reads with mapping quality below 30 were discarded and pcr duplicates were collapsed into consensus sequences. to estimate the misincorporation pattern at the end of the reads, bam files were run on mapdamage2.072. then, to test for the authenticity of the consensus sequences, we used a bayesian contamination estimate to calculate the probability that the recovered mtdna fragments come […]

2015
PMCID: 4472748

[…] and filtering for reads with a minimum qc score of 30, indicating 99.9% base call accuracy. samtools v0.1.19-96b5f2294a [32] was used to remove duplicates. damage patterns were assessed using the mapdamage tool [33] and normalized contamination estimates were calculated as in gamba et al. [8], we found substantial difference in both endogenous content and total endogenous dna yields […]

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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