Written Felix M Key

Contact the author at key [at] shh [dot] mpg [dot] de for any questions about this code or correspondence about this work.

This project is licensed under the terms of the CC BY.

This README provides an overview about the post-processing module of HOPS presented in:

Hübler, R., Key, F.M., et al. HOPS: automated detection and authentication of pathogen DNA in archaeological remains. Genome Biology 20, 280 (2019) doi: 10.1186/s13059-019-1903-0

Please cite this paper if any meaningful piece of the HOPS software is used.

Enjoy!

• R (tested on version 3.3.1 +)
• R libraries:
  • parallel
  • getopt
  • gridBase
  • gridExtra

Optional:

• R libraries:
  • jsonlite (if you want generate json-formatted raw heatmap data)

Postprocessing has to be done on the output data generated by HOPS::MALTextract (beta v1.3+). It iterates over relevant files produced, and summarises potential positive hits in a heatmap and detailed profile-pdfs (please also see profilePDF_explained.pdf). The heatmap data in TSV format is also created, and a JSON version can also be requested.

./postprocessing.AMPS.r -h
Usage: ./postprocessing.AMPS.r [-[-rmaex.out.fld|r] <character>] [-[-maltex.filter|m] [<character>]] [-[-threads|t] <double>] [-[-help|h]] [-[-node.list|n] <character>]
    -r|--rmaex.out.fld    MALTextract output folder.
    -m|--maltex.filter    MALTextract filter mode: <default,def_anc>. This script is not designed for 'scan' output. Default: <def_anc>.
    -t|--threads          Max number of cores used.
    -h|--help             Print this help.
    -n|--node.list        List (\n separated) of nodes to be reported on (aka input species/node list used for MALTextract).
    -j|--heatmap.json    Optional exporting of heatmap data in json format.

~/Documents/shh/sysEva/scripts/amps/postprocessing.AMPS.r \
-m def_anc \
-r HOPS/output/folder \
-t 16 \
-n /projects1/users/key/anc5h/soi.backup/List_of_pathogens_KB_fmk12_wViruses1.txt