NAME

debrief-42.pl - Summarize the results of a 42 metagenomic run

VERSION

version 0.213470

USAGE

    debrief-taxR-42.pl --indir=<indir> --in=<str> [optional arguments]

REQUIRED ARGUMENTS

--indir=<indir>

Path to input directory containing TAX-REPORT files.

--in[-strip]=<str>

Substring to strip from infile basenames to derive pre-42 filenames. This often corresponds to the out_suffix option of the YAML config file for 42 (e.g., -42).

OPTIONAL ARGUMENTS

--outdir=<dir>

Optional output dir that will contain the computed TSV files (will be created if needed) [default: none]. Otherwise, output files will be written in the working directory.

--out[-suffix]=<suffix>

Suffix to append to infile basenames for deriving outfile names [default: none].

--taxdir=<dir>

Path to local mirror of the NCBI Taxonomy database.

--seq_labeling=<file>

Path to custom IDL file providing low-level taxa for accurate labeling of the sequences newly added by 42 [default: none].

--contam_labeling=<file>

Path to custom IDL file providing high-level taxa for broad detection of contaminant sequences among new sequences [default: none].

--verbosity=<level>

Verbosity level for logging to STDERR [default: level.default]. Available levels range from 0 to 6. Level 6 corresponds to debugging mode.

--version

--usage

--help

--man

Print the usual program information

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

CONTRIBUTOR

Mick VAN VLIERBERGHE <mvanvlierberghe@doct.ulg.ac.be>

COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.