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 ‘NC_032001.1|tax|1917232|’), multiple species must be comma separated (e.g. -s ‘NC_032001.1|tax|1917232|,NC_031076.1|tax|1838137|,NC_034267.1|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.

-yaxis_dp_max MAX_VALUE
DamagePlot: Maximal y-axis value.

-color_c_t COLOR_C_T
DamagePlot: Color (HEX code) for C to T misincorporation frequency.

-color_g_a COLOR_G_A
DamagePlot: Color (HEX code) for G to A misincorporation frequency.

-color_insertions COLOR_C_T
DamagePlot: Color (HEX code) for base insertions.

-color_deletions COLOR_DELETIONS
DamagePlot: Color (HEX code) for base deletions.

-color_other COLOR_OTHER
DamagePlot: Color (HEX code) for other bases different to reference.

-only_merged
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.

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