---
name: "load2sqlitedb"
section: "1"
platform: "linux"
package: "augustus"
version: "3.5.0+dfsg-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/load2sqlitedb"
---

# load2sqlitedb(1)

load genome sequences and extrinsic evidence hints into a SQLite database

## NAME

load2sqlitedb - load genome sequences and extrinsic evidence hints into a SQLite database

## SYNOPSIS

**load2sqlitedb** \[OPTIONS\] --species=*SPECIES* --dbaccess=*database.db* *inputfilename*

## DESCRIPTION

**load2sqlitedb** is a tool to load genome sequences and extrinsic evidence hints into a SQLite database.\
 When storing genomes/hints of multiple organisms call this program repeatedly for each one.

## OPTIONS

*inputfilename* refers to a genome file in FASTA format or a hints file in GFF format.

### Mandatory options

- **-s**, **--species**=*SPECIES*

  SPECIES is a name for your species and the same identifier as is used in the treefile and alnfile parameters to augustus.

- **-d**, **--dbaccess**=*database.db*

  The file name of the SQLite database that will be opened or created if it does not already exist.

### Additional options

- **-c**, **--chunksize**=*size*

  This option is only relevant when loading a sequence file.\
   The sequences in the input genome are split into chunks of this size so that subsequent retrievals of small sequence ranges do not require to read the complete - potentially much longer - chromosome. (⇐ 1000000). Default Value: 50000

- **-i**, **--noIdx**

  Use this flag to suppress the building of indices on the database tables.\
   If you are going to load several genomes and/or hint files in a row, this option is recommended to speed up the loading. But make sure to build indices with --makeIdx after all genomes/hints are loaded. Otherwise, data retrieval operations can be very slow.

- **-m**, **--makeIdx**

  Use this flag to build the indices on the database tables after loading several genomes and/or hint files with --noIdx.\
   Only call this once for all species, e.g. load2sqlitedb --makeIdx --dbaccess=database.db

- **-r**, **--clean**

  Makes a clean load deleting existing hints/genome for the species from the database.+ When called with a gff file, only the hints for the species are delete, but not the genome.\
   When called with a fasta file, both hints and genome for the species are deleted.

- **-h**, **--help**

  Produce help message.

## EXAMPLE

```
  load2sqlitedb --species=mouse --dbaccess=vertebrates.db mouse.fa
  load2sqlitedb --species=mouse --dbaccess=vertebrates.db mouse.hints.gff
  load2sqlitedb --species=human --dbaccess=vertebrates.db human.fa
  load2sqlitedb --species=human --dbaccess=vertebrates.db human.hints.gff
```

## AUTHORS

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