There are three main areas where MIRA could need help: documentation,
programming and resources. If you feel you can help, please contact
bach@chevreux.org


Documentation
=============
- writing beginner tutorials for assembling data (including preprocessing
  steps with other programs like lucy, pregap4 etc) would be really, REALLY
  welcome. Especially for the usage of third party scripts.
- do you have a special use case for MIRA and would like to write a
  walk-through? Please do, this would be *much* appreciated.



Programming
===========
- a linear-space banded Smith-Waterman alignment routine that works without
  runtime-penalty would come in handy. I already have an idea how to realise
  this but no time. Tricky, but feasible.
- testing compilation and running of MIRA on presently untested platforms
  (see INSTALL for a list of platforms).
- some helper scripts to automatically download, quickly reformat and then
  assemble data from the NCBI SRA & trace archive or the ENSEMBL trace server
  would be nice (perl or  Tcl preferred)
- multithreading: the Smith-Waterman alignments could be calculated in
  parallel (not trivial, but should not be really hard either). Furthermore,
  the task of building contigs could be distributed on 2 threads or even 2
  threads per independent contig (harder to realise). I did not find the time
  to build this in yet.
- and of course: feedback in any form, be it ideas, bug reports, success
  stories (or failures) etc.


Resources:
==========
My trusted i940 system at home has 24 GiB RAM which sometimes is a bit
... small. Anyone who wants to sponsor an Intel Core i7-3960X system with 64
GiB RAM? Just kidding, I don't really need it atm ;-)
