Perform splitting of Oxford Nanopore sequencing data in a fail and pass dataset using a user defined quality cutoff. The script can read compressed input and will write to gzip compressed files.
pip install NanoSplit
NanoSplit [-h] [-q QUALITY] [--outdir OUTDIR] fastqfile
Required arguments:
fastqfile Fastq file to split, can be gz compressed.
Optional arguments:
-h, --help show this help message and exit
-q QUALITY, --quality QUALITY
Splitting on this average read quality score
Default: 12
--outdir OUTDIR Specify directory in which output has to be created.
NanoSplit reads.fastq.gz
NanoSplit -q 6 reads.fastq.gz
NanoSplit -q 10 --outdir /home/user/datasetsplit/ reads.fastq