demort 0.2.4

DEmultiplexing MOnitoring Report Tool

demort evaluates demultiplexed fastq files by computing various metrics.

DEPENDENCIES

You need to install python 3.7 and depencies. Check version by typing on:

python3 --version

python3 depencies :

• joblib
• biopython
• matplotlib

USAGE

demort check fastq files into specified folder(s) then count number of reads for each fastq files for each folder and finally return a summary csv table and a pdf boxplot picture.

(process a list of folder as a strings)

demort.py -d folder/folder1,folder/folder2,folder/folder3 \
 -t 8 \
 -p results.pdf \
 -o results.csv

(process a list of folder into a file)

demort.py -d example/folder_to_process.txt \
 -t 8 \
 -p results.pdf \
 -o results.csv

COMMAND-LINE ARGUMENTS

complete flag argument	short flag	Default value	Summary
--inputFolder	-d	NA	a string of folderpath separated by coma , OR a file containing a list
--threads	-t	1	Number of available cores
--output_pdf	-p	NA	path of the file where to write a pdf boxplot picture
--output_csv	-o	NA	path of the file where to write a csv table

INPUT

folder/
├── folder1
│   ├── fqfileA.fq.gz
│   ├── fqfileB.fq.gz
│   └── fqfileC.fq.gz
├── folder2
│   ├── fqfileD.fq.gz
│   └── fqfileE.fq.gz
└── folder3
    ├── fqfileF.fq.gz
    ├── fqfileG.fq.gz
    └── fqfileH.fq.gz

OUTPUTS

• summary csv table [foldername, filename, number of reads]
• pdf boxplot picture

SYSTEM REQUIREMENTS

Linux (64-bit and 32-bit with slightly limited functionality) and macOS (OS X) are supported.