fastq-handler 0.1.3

A python module to process minion fastq files by concatenating reads as they are generated

Fastq Handler

A python module to process ONT fastq files by concatenating reads as they are generated during a sequencing run

INTRODUCTION

The fastqc-handler module screens folders and subfolders for fastq (fastq or fastq.gz format) files and concatenates them iteratively. This is useful for merging same-sample reads that are split into multiple files, as commonly obtained in ONT sequencing. The output is a one file per output fastq.gz, containing all reads from the previous files. The output directory structure is maintained.

INPUT

A directory containing fastq files. The files can be in subfolders (each representing a different sample). The files can be gzipped or not.

USAGE

usage: fastq_handler [-h] [-i INPUT] [-o OUTPUT] [-n TAG] [--keep_names]

parse arguments

optional arguments:
    -h, --help            show this help message and exit
    -i INPUT, --input INPUT
                        Input directory
    -o OUTPUT, --output OUTPUT
                        Output directory
    -n TAG, --tag TAG     Tag to add to output file name
    --keep_names          Keep original file names in output file
    --max-size MAX_SIZE   max size of the output file, in kilobytes

REQUIREMENTS

Modules

• dataclasses==0.6
• natsort==8.3.1
• pandas==1.5.3
• setuptools==57.4.0
• xopen==1.7.0

INSTALLATION

python -m venv .venv
source .venv/bin/activate
python -m pip install fastq-handler

MAIN OUTPUTS

Note: The output directory structure is maintained.

• fastq.gz files containing all reads from the previous files.
• log.txt file containing the concatenation process.

Maintainers

• @xiaodre21
• @santosjgnd
• @insaflu