A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage

DamageProfiler

This method can be used to calculate damage profiles of mapped ancient DNA reads.

Main author: Judith Neukamm judith.neukamm@uzh.ch\Contributor: Alexander Peltzer, James A. Fellows Yates, and Alexander Hübner.

Citation

If you use the tool, please cite the publication:

DamageProfiler Neukamm, J., Peltzer, A., & Nieselt, K. (2020). DamageProfiler: Fast damage pattern calculation for ancient DNA. Bioinformatics (btab190). https://doi.org/10.1093/bioinformatics/btab190

Method

DamageProfiler calculates damage profiles of mapped reads and provides a graphical as well as text based representation.

It creates - damage plots- fragment length distribution- read identity distribution - base frequency table of reference - table of different base misincorporations and their occurrences

How to run

java -jar DamageProfiler-VERSION.jar -i input_file -o output_folder [options]

Running the jar file without any parameter starts the GUI to configure the run.

-h, --help\Shows this help page.\\-v, --version\Shows the version of DamageProfiler.\\-i INPUT\The input sam/bam/cram file (Required).\\-o OUTPUT\The output folder (Required).\\-r REFERENCE\The reference file (fasta format).\\-t THRESHOLD\DamagePlot: Number of bases which are considered for plotting nucleotide misincorporations. Default: 25.\\-s SPECIES\Reference sequence name (Reference sequence name (SN tag) of the SAM record). Species must be put in quotation marks (e.g. -s 'NC032001.1|tax|1917232|'), multiple species must be comma separated (e.g. -s 'NC032001.1|tax|1917232|,NC031076.1|tax|1838137|,NC034267.1|tax|1849328|'). Commas within the reference sequence name are not allowed. Please specify either -s or -sf.\\-sf FILE SPECIES\Text file containing a list with species (Reference sequence name (SN tag) of the SAM record, one per line) for which damage profile has to be calculated. Please specify either -s or -sf.\\-l LENGTH\Number of bases which are considered for frequency computations. Default: 100.\\-title TITLE\Title used for all plots. Default: input filename.\\-yaxisdpmax MAXVALUE\DamagePlot: Maximal y-axis value.\\-colorct COLORCT\DamagePlot: Color (HEX code) for C to T misincorporation frequency.\\-colorga COLORGA\DamagePlot: Color (HEX code) for G to A misincorporation frequency.\\-colorinsertions COLORCT\DamagePlot: Color (HEX code) for base insertions.\\-colordeletions COLORDELETIONS\DamagePlot: Color (HEX code) for base deletions.\\-colorother COLOROTHER\DamagePlot: Color (HEX code) for other bases different to reference.\\-onlymerged\Use only mapped and merged (in case of paired-end sequencing) reads to calculate damage plot instead of using all mapped reads. The SAM/BAM entry must start with 'M', otherwise it will be skipped. Default: false.\\-sslib\Single-stranded library protocol was used. Default: false.

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A more detailed documentation of DamageProfiler is available at https://damageprofiler.readthedocs.io.

To restore the repository download the bundle

wget https://archive.org/download/github.com-Integrative-Transcriptomics-DamageProfiler_-_2021-04-26_07-35-31/Integrative-Transcriptomics-DamageProfiler_-_2021-04-26_07-35-31.bundle

and run:

 git clone Integrative-Transcriptomics-DamageProfiler_-_2021-04-26_07-35-31.bundle 

Source: https://github.com/Integrative-Transcriptomics/DamageProfiler
Uploader: Integrative-Transcriptomics
Upload date: 2021-04-26

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