Minimus

Overview

Minimus is an assembly pipeline designed specifically for small data-sets, such as the set of reads covering a specific gene. Note that the code will work for larger assemblies (we have used it to assemble bacterial genomes), however, due to its stringency, the resulting assembly will be highly fragmented. For large and/or complex assemblies the execution of Minimus should be followed by additional processing steps, such as scaffolding.

Minimus follows the Overlap-Layout-Consensus paradigm and consists of three main modules which share information through a central file bank:

• hash-overlap - Computes the overlaps between the reads using a modified version of the Smith-Waterman local alignment algorithm
• tigger - Uses the read overlaps to generate the layouts of reads representing individual contigs
• make-consensus - Refines the layouts produced by the tigger to generate accurate multiple alignments within the reads

Minimus uses AMOS message files as both the inputs and the outputs. Please see the File conversion utilities documentation for more information.

Minimus2 is a modified version of the minimus pipeline designed for merging two sequence sets. Instead of hash-overlap it uses a nucmer based overlap detector which is much faster.

Documentation

Documentation on running minimus is included with the distribution in the /docs subdirectory.

See Minimus/README.

Examples

Examples of a flu assembly and a Zebrafish gene can be found in the test/minimus directory created when the AMOS distribution is untarred. Documentation on the examples is included with the distribution in /docs/minimus.README.

Basic usage

To run minimus will you need a set of sequence files. Assuming you have a set of reads in fasta format called my_reads.seq, you can run minimus with the following two commands:

`toAmos -s my_reads.seq -o my_reads.afg'

`minimus my_reads'

The output will be a fasta formatted file called '"my_reads.fasta"', a contig file with details about the assembly of each contig called '"my_reads.contig"', and an AMOS bank folder with various files used internally by minimus. The toAmos file conversion utility is the most general and probably the most useful of the file conversion utilities included with minimus. More information about toAmos and the other file conversion utilities can be found in the AMOS documentation wiki. For example, you can include quality data from a Phred style quality score file by running toAmos with the -q option as follows:

`toAmos -s my_reads.fasta -q my_reads.qual -o my_reads.afg'

Minimus can also be called with the following equivalent command:

`runAmos -C $AMOSBASE/src/Pipeline/minimus.acf my_reads'

The AMOS package also includes other helpful tools such as Hawkeye, which is useful for evaluating your assembly with respect to paired-end reads. It can be run on the minimus bank with the following command:

`hawkeye my_reads.bnk/'

Publication

Minimus: a fast, lightweight genome assembler

Sommer, DD, Delcher, AL, Salzberg, SL, and Pop, M. (2007) BMC Bioinformatics, 8:64doi:10.1186/1471-2105-8-64.

Acknowledgements

The development of minimus was supported by the National Institutes of Health under grants R01-LM06845 and R01-LM007938 to SLS and by Department of Homeland Security cooperative agreement W81XWH-05-2-0051.