---
name: "Honey"
section: "1"
platform: "linux"
package: "pbhoney"
version: "15.8.24+dfsg-7"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/Honey"
---

# Honey(1)

genomic structural variation discovery

## NAME

Honey - genomic structural variation discovery

## SYNOPSIS

**Honey** {*subcommand*}*\[*options*\]*

## DESCRIPTION

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

## OPTIONS

For a complete description, see the help menu

- **-h, --help**

  Show summary of options.

## SEE ALSO

[**blasr**(1)](/blasr/1.md)\
 /usr/share/doc/pbhoney/HoneyReadme.txt