This is a modified version of the original Kraken program. Modified from the original on October 4, 2016. MODIFICATIONS: classify.cpp seqreader.cpp seqreader.hpp
ADDITIONS: fqmapper.cpp fqmapper.h gzstream.cpp gzstream.h
These modifications allow for the classify module to read directly from gzipped paired- or single- end fastq files. Additionally, if supplied with a divisions files, classify will split the fastqs into separate fastq files based on the taxnomic classification of the read(s).
Example usage: classify -M -p <DIVISIONS_FILE> -t -f -d <LOCATION OF DATABASE .kdb FILE> -i <LOCATION OF DATABASE .idx FILE> -x <OUTPUT_PREFIX> -n -2
EXAMPLE DIVISIONS FILE (tab-delimited) hsap 9606 mmus 10090,39107,337687
For documentation on the full functionality of the original software, please see the original documentation below.
Please see the Kraken webpage or the Kraken manual
for information on installing and operating Kraken.
A local copy of the Kraken manual is also present here
in the docs/ directory (MANUAL.html and MANUAL.markdown).