---
name: "LAindex"
section: "1"
platform: "linux"
package: "daligner"
version: "1.0+git20180524.fd21879-1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/daligner"
---

# LAindex(1)

local alignment discovery between long nucleotide sequencing reads

Part of [daligner(1)](/daligner/1.md).

## NAME

daligner - local alignment discovery between long nucleotide sequencing reads

## SYNOPSIS

**daligner** \[*options*\] *files*...

## DESCRIPTION

These tools permit one to find all significant local alignments between reads encoded in a Dazzler database. The assumption is that the reads are from a Pacific Biosciences RS II long read sequencer. That is, the reads are long and noisy, up to 15% on average.

## OPTIONS

For a complete description of available commands and their options, see /usr/share/doc/daligner/README.md