# README2
fRep.zip is a zip file containing the full analysis results by PATHDET.
All file names are prefixed with Run-ID.

## File list
(1)  'PREFIX'_report.txt
(2)  'PREFIX'.full.html
(3)  'PREFIX'_fK.txt
(4)  'PREFIX'_fP.txt
(5)  'PREFIX'_fF.txt
(6)  'PREFIX'_fG.txt
(7)  'PREFIX'_fS.txt
(8)  'PREFIX'_Fungi.txt
(9)  'PREFIX'_Virus.txt
(10) 'PREFIX'_amr.txt
(11) 'PREFIX'_QCreport
(12) 'PREFIX'_log.txt
(13)  readme2.txt

## File contents
(1) 'PREFIX'_report.txt
A text file describing full analysis results by PATHDET.

(2) 'PREFIX'_full.html
Krona HTML file made from PARHDET full analysis results.
See [Krona] (https://github.com/marbl/Krona/wiki) website for detail on Krona chart.

'PREFIX'_p'TAXON'.txt
A tab-delimited file describing the number of raw reads, number of sequencing reads per million mapped reads (RPM), and relative abundance (RA) of the individual microorganisms.
The microorganism name is described with the rank of 'TAXON'.
(3) K: kingdom
(4) P: phylum
(5) F: family
(6) G: genus
(7) S: species

(8) 'PREFIX'_Fungi.txt
A tab-delimited file describing the number of raw reads, RPM and RA of fungi.

(9) 'PREFIX'_Virus.txt
A tab-delimited file describing the number of raw reads, RPM and RA of virus.

(10) 'PREFIX'_amr.txt
A tab-delimited file describing drug name, the number of raw reads and RPM of antimicrobial resistance gene.

(11) multiqc_files (6files)
"multiqc_" files containing MultiQC HTML file and its configuration files.
MultiQC compares the quality control for input fastq file with the preprocessed fastq file.
See [MultiQC] (https://multiqc.info/) website for detail on MultiQC report.

(12) 'PREFIX'_log.txt
A log file describing the time required for each analysis part in PATHDET.
The number of readings processed for each analysis part in PATHDET is also briefly reported.

## License
[Department of Genetics, Research Institute of Environmental Medicine, Nagoya University](http://www.riem.nagoya-u.ac.jp/4/genetics/index.html)
