Calculate statistics for Oxford Nanopore sequencing data and alignments
Project description
Calculate various statistics from an Oxford Nanopore dataset in fastq, bam or albacore sequencing summary format.
INSTALLATION
pip install nanostat
USAGE
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
Example output
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%
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