barcodeSpliter
"barcodeSpliter" is a simple command-line tool that can split the mix-sampled sequencing by the barcode label, that is, demultiplex the sample. Currently at version V1.6, I have implemented this functionality most directly due to optimization issues that may require you to run more memory than the sequenced files.
Installation
# simple run
pip install barcodeSpliter
# if need upgrade
pip install -U barcodeSpliter
E.g.:
barcodeSpliter ./example_data/test_r1.fastq.gz ./example_data/test_r2.fastq.gz ./example_data/barcode.tsv
TO DO LIST:
- support large sequencing files.
- support muti-threads
- add function: statistic barcode.
Usage
usage: barcodeSpliter [-h] [-sr SEARCHREGION] [-o OUTFOLDER] r1.fastq.gz r2.fastq.gz barcode.csv
This software can use barcode label to separate different samples in mixed-sample sequencing.
positional arguments:
r1.fastq.gz Sequencing reads, R1. Also support uncompressed format, like: r1.fastq
r2.fastq.gz Sequencing reads, R2. Also support uncompressed format, like: r2.fastq
barcode.csv csv file contains barcode info. eg:Barcode01,TAACTCGG,TAACAGTT
optional arguments:
-h, --help show this help message and exit
-sr SEARCHREGION, --searchRegion SEARCHREGION
Barcode search region.Default is 20, means the first 20nt of reads.
-o OUTFOLDER, --outfolder OUTFOLDER
The name of output folder can be customized. Default: ./Output/