Calculate various statistics from an Oxford Nanopore dataset in fastq, bam or albacore sequencing summary format.
pip install nanostator
conda install -c bioconda nanostat
NanoStat [-h] [-v] [-o OUTDIR] [-p PREFIX] [-t THREADS]
(--fastq FASTQ | --summary SUMMARY | --bam BAM)
Get statistics of Oxford Nanopore read dataset.
Mandatory one of the following data sources:
--fastq FASTQ Data is in fastq format.
--summary SUMMARY Data is a summary file generated by albacore.
--bam BAM Data as a sorted bam file.
Optional arguments:
-h, --help show this help message and exit
-v, --version Print version and exit.
-o, --outdir OUTDIR Specify directory in which output has to be created.
-p, --prefix PREFIX Specify an optional prefix to be used for the output files.
-t, --threads THREADS Set the allowed number of threads to be used by the script
Number of reads: 408254
Total bases: 3508315665
Median read length: 5168.0
Mean read length: 8593.46
Readlength N50: 39346
Top 5 read lengths and their average basecall quality score:
Length: 255821bp Q: 6.84
Length: 254573bp Q: 7.09
Length: 253711bp Q: 6.96
Length: 245784bp Q: 6.98
Length: 245776bp Q: 7.06
Top 5 average basecall quality scores and their read lengths:
Length: 407bp Q: 16.22
Length: 880bp Q: 16.18
Length: 729bp Q: 16.12
Length: 1057bp Q: 16.08
Length: 841bp Q: 15.84
Number of reads and fraction above quality cutoffs:
Q5: 406428 99.55%
Q10: 305509 74.83%
Q15: 124 0.03%
Q20: 0 0.0%