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:
       -h, --help
              show the help and exit

       -v, --version
              Print version and exit.

       -o, --outdir OUTDIR
              Specify directory for output, only in combination with -n.

       -p, --prefix PREFIX
              Specify an optional prefix to be used for the output file.

       -n, --name NAME
              Specify a filename/path for the output, stdout is the default.

       -t, --threads N
              Set the allowed number of threads to be used by the script.

       --tsv  Output the stats as a properly formatted TSV.

   Input options.:
       --barcoded
              Use if you want to split the summary file by barcode

       --readtype {1D,2D,1D2}
              Which read type to extract information about from summary. Options are 1D, 2D, 1D2

   Input data sources, one of these is required.:
       --fastq file [file ...]
              Data is in one or more (compressed) fastq file(s).

       --fasta file [file ...]
              Data is in one or more (compressed) fasta file(s).

       --summary file [file ...]
              Data is in one or more (compressed) summary file(s)generated by albacore or guppy.

       --bam file [file ...]
              Data is in one or more sorted bam file(s).

       --ubam file [file ...]
              Data is in one or more unmapped bam file(s).

       --cram file [file ...]
              Data is in one or more sorted cram file(s).

       --feather file [file ...]
              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.

NanoStat 1.4.0                                     April 2025                                        NANOSTAT(1)