NanoStat - manual page for NanoStat 1.4.0
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.
-
-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.
- --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
-
--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).
- 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
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.