NanoStat1

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