---
name: "snap-aligner"
section: "1"
platform: "linux"
package: "snap-aligner"
version: "2.0.3+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/snap-aligner"
---

# snap-aligner(1)

scalable nucleotide alignment program

## NAME

snap-aligner - scalable nucleotide alignment program

## SYNOPSIS

**snap-aligner** *\<command\>* \[*\<options\>*\]

## DESCRIPTION

Welcome to SNAP version 2.0.3.

### Commands:

- index

  build a genome index

- single

  align single-end reads

- paired

  align paired-end reads

- daemon

  run in daemon mode--accept commands remotely

Type a command without arguments to see its help.