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DEmultiplexing MOnitoring Report Tool

Project description

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 :

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.

Project details


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Files for demort, version 0.2.4
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Supported by

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