README.md

ATG_fastq_merger

This script uses FLASH with default parameters to merge paired-end illumina reads.

Requirements

• flash package: can be installed via conda.
• python3
• Tested on a linux machine, no reason to not to work on Mac and Windows.

Usage

Single sample

python merger.py [--sample-name SAMPLE_NAME] [--read1 READ1] [--read2 READ2] [--out-dir PATH_TO_OUTPUT_DIR]

or

python merger.py [-n SAMPLE_NAME] [-r1 READ1] [-r2 READ2] [-o PATH_TO_OUTPUT_DIR]

A list of samples:

Prepare a tab delimited SAMPLES_TSV file with the following headers sample_name,read1,read2. For example:

sample_name	read1	read2
mysample_1	whatever1.R1.fastq.gz	whatever1.R2.fastq.gz
mysample_2	whatever2.R1.fastq.gz	whatever2.R2.fastq.gz

python merger.py [--samples-file PATH_TO_SAMPLES_TSV] [--out-dir PATH_TO_OUTPUT_DIR]

or

python merger.py [-f PATH_TO_SAMPLES_TSV] [-o PATH_TO_OUTPUT_DIR]

Important Note: sample_name must be alphanumeric (i.e., avoid &, $, @, -, %, * and empty space in the file names).

Outputs

• out_dir/sample_name.fastq contains the fastq file(s).
• out_dir/merger_stats.tsv contains the FLASH statistics (TotalPairs, CombinedPairs, UncombinedPairs, PercentCombined) per sample.

References

• FLASH : Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011 Nov 1;27(21):2957-63. doi: 10.1093/bioinformatics/btr507. Epub 2011 Sep 7. PMID: 21903629; PMCID: PMC3198573.

Bugs

Please report errors/bugs to: Amir.Taheri.Ghahfarokhi@gmail.com