Difference between revisions of "Minimus"

Revision as of 08:56, 31 July 2009

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:

• 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 as AMOS messages 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 example

Assuming you have a set of reads in fasta format called my_reads.fasta, and an associated set of read quality scores (in the same order?) called my_reads.qual (Note that in general, Amos expects Phred style quality scores ????).

toAmos \
  -s my_reads.fasta \
  -q my_reads.qual \
  -o my_reads.afg

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

...

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.