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
conda install -c bioconda 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. Specifying a list of files of the same type is supported. Optional arguments: --readtype Specify read type to extract from summary file Options: 1D (default), 2D or 1D2 -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. -n, --name NAME Specify a custom filename/path for the output, <stdout> for printing to stdout. -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 This only applies to bam and fastq format as data source
STATUS
Example output
Number of reads: 99875 Total bases: 779100562 Median read length: 5456.0 Mean read length: 7800.76 Readlength N50: 12658 Top 5 read lengths and their average basecall quality score: Length: 299625bp Q: 10.36 Length: 272879bp Q: 9.99 Length: 271441bp Q: 10.94 Length: 261038bp Q: 8.0 Length: 250267bp Q: 7.74 Top 5 average basecall quality scores and their read lengths: Length: 1455bp Q: 16.54 Length: 3634bp Q: 16.48 Length: 733bp Q: 16.23 Length: 515bp Q: 16.2 Length: 909bp Q: 15.89 Number of reads and fraction above quality cutoffs: Q5: 88489 88.6% Q10: 61809 61.89% Q15: 175 0.18% Q20: 0 0.0% Data produced using 512 active channels. Data was produced in run(s) with ID: 002dc25e406b22dd8e4d2a5ee83dcbb67072e10d 005aaa922c42c455c07a472a9c30f0209f1b0d93 00b31b64541f79ff1f562c3e3602d3f265cd3b05 00c9faabd00f4676a2255da178a62c1fe6ae061b 00f9dec9cb591f4cb4c60c129f87faf731323386
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