A customisable FastQ Demuxer
Project specific FastQ demultiplexer. Of limited general use, but existing code can be easily
changed according to needs. Contains plenty of hardcoded assumptions, e.g. barcodes are of length 6
and names start with “ROW”. Provided barcodes come from the Fluidigm C1 mRNA Seq HT Demultiplex
Script.
Install nim. Then run nimble build
$ ./fluidemux -h
Usage:
main [required&optional-params]
Options(opt-arg sep :|=|spc):
-h, --help write this help to stdout
-1=, --fastq1= string REQUIRED FastQ1
-2=, --fastq2= string REQUIRED FastQ2
-b=, --barcodeYaml= string REQUIRED YAML file with barcodes to name mapping
-o=, --outpref= string REQUIRED Output prefix