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Name

loadAssembly.pl - Wrapper script to load/unload an assembly to/from Smash database

Synopsis

        loadAssembly.pl [options]

Options

--assembly

Name of assembly to load into Smash database. This assembly should exist in Smash repository. This script will then load it into the database.

--unload

Unloads the entries corresponding to this assembly from the database. This enables you to reload the assembly from the files in Smash repository. Use this when you suspect something wrong in the database, but you think the assembly itself is fine. In such cases, you --unload the assembly and then load it again using this script.

--wipeout

Unloads the entries corresponding to this assembly from the database and removes all the files from the Smash repository. Once an assembly is wipedout, it disappears from Smash. So please be careful when you use this option.

--help

Prints this manual.

Description

loadAssembly.pl is a wrapper script to load an assembly in Smash repository into Smash database. The assembly should already exist in the repository and must have been generated by a Smash-compatible script such as doAssembly.pl.

A typical use of loadAssembly.pl follows doAssembly.pl, like so:

        doAssembly.pl --metagenome=MC20.MG1 --assembler=Arachne \
            --genome_size=20000 --superiterative
        loadAssembly.pl --assembly=MC20.MG1.AS1

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