---
name: "NanoStat"
section: "1"
platform: "linux"
package: "python3-nanostat"
version: "1.4.0-3"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/NanoStat"
---

# NanoStat(1)

manual page for NanoStat 1.4.0

## 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.