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NANOSTAT(1) User Commands NANOSTAT(1)

NAME

NanoStat - manual page for NanoStat 1.4.0

DESCRIPTION

usage: NanoStat [-h] [-v] [-o OUTDIR] [-p PREFIX] [-n NAME] [-t N] [--tsv]

[--barcoded] [--readtype {1D,2D,1D2}] (--fastq file [file ...] | --fasta file [file ...] | --summary file [file ...] | --bam file [file ...] | --ubam file [file ...] | --cram file [file ...] | --feather file [file ...])

Calculate statistics of long read sequencing dataset.

General options:

show the help and exit
Print version and exit.
Specify directory for output, only in combination with -n.
Specify an optional prefix to be used for the output file.
Specify a filename/path for the output, stdout is the default.
Set the allowed number of threads to be used by the script.
Output the stats as a properly formatted TSV.

Input options.:

Use if you want to split the summary file by barcode
Which read type to extract information about from summary. Options are 1D, 2D, 1D2

Input data sources, one of these is required.:

Data is in one or more (compressed) fastq file(s).
Data is in one or more (compressed) fasta file(s).
Data is in one or more (compressed) summary file(s)generated by albacore or guppy.
Data is in one or more sorted bam file(s).
Data is in one or more unmapped bam file(s).
Data is in one or more sorted cram file(s).
Data is in one or more feather file(s).

EXAMPLES:

NanoStat --fastq reads.fastq.gz --outdir statreports NanoStat --summary sequencing_summary1.txt sequencing_summary2.txtsequencing_summary3.txt --readtype 1D2 NanoStat --bam alignment.bam alignment2.bam

SEE ALSO

The full documentation for NanoStat is maintained as a Texinfo manual. If the info and NanoStat programs are properly installed at your site, the command

info NanoStat

should give you access to the complete manual.

December 2020 NanoStat 1.4.0