What it does

Runs MIRA v4.0 in de novo mode, collects the output, generates a sorted BAM file, and then throws away all the temporary files.

MIRA is an open source assembly tool capable of handling sequence data from a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent and also PacBio).

It is particularly suited to small genomes such as bacteria.

Notes on paired reads

MIRA uses read naming conventions to identify paired read partners (and does not care about their order in the input files). In most cases, the Solexa/Illumina setting is fine. For Sanger capillary sequencing, you may need to rename your reads to match one of the standard conventions supported by MIRA. For Roche 454 or Ion Torrent the appropriate settings depend on how the FASTQ file was produced:

• If using Roche's sffinfo or older versions of sff_extract to convert SFF files to FASTQ, your reads will probably have the ---> <--- orientation and use the .f and .r suffixes (FR naming).
• If using a recent version of sff_extract, then the /1 and /2 suffixes are used (Solexa/Illumina style naming) and the original 2---> 1---> orientation is preserved.

The reason for this is the raw data for Roche 454 and Ion Torrent paired-end libraries sequences a circularised fragment such that the raw data begins with the end of the fragment, a linker, then the start of the fragment. This means both the start and end are sequenced from the same strand, and have the orientation 2---> 1--->. However, in order to use the data with traditional tools expecting Sanger capillary style ---> <--- orientation it was common to reverse complement one of the pair to mimic this.

Citation

If you use this Galaxy tool in work leading to a scientific publication please cite the following papers:

Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 http://dx.doi.org/10.7717/peerj.167

Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999). Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html

This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler