---
name: "compileSpliceCands"
section: "1"
platform: "linux"
package: "augustus"
version: "3.5.0+dfsg-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/compileSpliceCands"
---

# compileSpliceCands(1)

Find introns parsing a set of exon candidates in GFF format

## NAME

compileSpliceCands - Find introns parsing a set of exon candidates in GFF format

## SYNOPSIS

**compileSpliceCands** -f \<splice candidates filename\> -g \<genome filename\>

## OPTIONS

### Parameters:

- **-f** \<filename\>

  potential splice sites in gff format

- **-g** \<filename\>

  genome file in fasta format

- **-c** \<integer\>

  defines the number of potential splice site every potential splice site itself is compared with

- **-t** \<float\>

  has to be between 0 and 1 and  defines how much the average coverage may differ

- **-m** \<integer\>

  defines how many bases around the splice site should be checked

- **-d**

  enables debugging output

- **-i** \<integer\>

  maximum length an Intron can be, default 500000 (human genome)

## AUTHORS

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.

## ADDITIONAL DOCUMENTATION

An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz.