Calculate statistics for Oxford Nanopore sequencing data and alignments
Project description
Calculate various statistics from a long read sequencing dataset in fastq, bam or albacore sequencing summary format.
INSTALLATION
USAGE
NanoStat [-h] [-v] [-o OUTDIR] [-p PREFIX] [-t THREADS] (--fastq FASTQ | --summary SUMMARY | --bam BAM) 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
EXAMPLES
NanoStat --fastq reads.fastq.gz --outdir statreports NanoStat --summary sequencing_summary1.txt sequencing_summary2.txt sequencing_summary3.txt --readtype 1D2 NanoStat --bam alignment.bam alignment2.bam``` ### 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 ```
I welcome all suggestions, bug reports, feature requests and contributions. Please leave an issue or open a pull request. I will usually respond within a day, or rarely within a few days.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.