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.