What it does

Runs the mirabait utility from MIRA v4.0 to filter your input reads according to whether or not they contain perfect kmer matches to your bait file. By default this looks for 31-mers (kmers or k-mers where the fragment length k is 31), and only requires a single matching kmer.

The mirabait utility is useful in many applications and pipelines outside of using the main MIRA tool for assembly or mapping.

Note mirabait cannot be used on protein (amino acid) sequences.

Example Usage

To remove over abundant entries like rRNA sequences, run mirabait with known rRNA sequences as the bait and select the negative matches.

To do targeted assembly by fishing out reads belonging to a gene and just assemble these, run mirabait with the gene of interest as the bait and select the positive matches.

To iteratively reconstruct mitochondria you could start by fishing out reads matching any known mitochondrial sequence, assembly those, and repeat.

Notes on paired read

While MIRA 4.0 is aware of many read naming conventions to identify paired read partners, this version of the mirabait tool considers each read in isolation. Applying it to paired read files may leave you with orphaned reads.

The version of mirabait included in MIRA 4.9.5 onwards is pair-aware.

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 https://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