---
name: "sublong"
section: "1"
platform: "linux"
package: "subread"
version: "2.0.8+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sublong"
---

# sublong(1)

toolkit for processing next-gen sequencing data

## NAME

sublong - toolkit for processing next-gen sequencing data

## DESCRIPTION

Please specify the input, output files and the index.

Sublong v2.0.4

Usage:

./sublong \[options\] **-i** \<index\_name\> **-r** \<input\> **-o** \<output\>

\## Mandatory arguments:

- **-i** \<string\>

  Base name of the index. The index must be built as a full index and has only one block.

- **-r** \<string\>

  Name of an input read file. Acceptable formats include gzipped FASTQ and FASTQ (automatically identified).

- **-o** \<string\>

  Name of an output file in BAM format.

\## Optional arguments: # input reads and output

- **--SAMoutput**

  Save mapping results in SAM format.

\# number of CPU threads

- **-T** \<int\>

  Number of CPU threads used. 1 by default.

\# others

- **-v**

  Output version of the program.

- **-X**

  Turn on the RNA-seq mode.

Refer to Users Manual for detailed description to the arguments.

## AUTHOR

 This manpage was written by Alexandre Mestiashvili for the Debian distribution and\
  can be used for any other usage of the program.