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<preface><title>Preface</title>
<blockquote>
  <attribution>Solomon Short</attribution>
  <para>
    <emphasis><quote>How much intelligence does one need to sneak upon lettuce?
    </quote></emphasis>
  </para>
</blockquote>
<para>
  This "book" is actually the result of an exercise in self-defense. It
  contains texts from several years of help files, mails, postings, questions,
  answers etc.pp concerning MIRA and assembly projects one can do with it.
</para>
<para>
  I never really intended to push MIRA. It started out as a PhD thesis and I
  subsequently continued development when I needed something to be done which
  other programs couldn't do at the time. But MIRA has always been available
  as binary on the Internet since 1999 ... and as Open Source since
  2007. Somehow, MIRA seems to have caught the attention of more than just a
  few specialised sequencing labs and over the years I've seen an ever growing
  number of mails in my inbox and on the MIRA mailing list. Both from people
  having been "since ever" in the sequencing business as well as from labs or
  people just getting their feet wet in the area.
</para>
<para>
  The help files -- and through them this book -- sort of reflect this
  development. Most of the chapters<footnote><para>Avid readers of David
  Gerrold will certainly recognise the quotes from his books at the beginning
  of each chapter</para></footnote> contain both very specialised
  topics as well as step-by-step walk-throughs intended to help people to get
  their assembly projects going. Some parts of the documentation are written
  in a decidedly non-scientific way. Please excuse, time for rewriting mails
  somewhat lacking, some texts were re-used almost verbatim.
</para>
<para>
  The last few years have seen tremendous change in the sequencing
  technologies and MIRA 4 reflects that: core data structures and
  routines had to be thrown overboard and replaced with faster and/or more
  versatile versions suited for the broad range of technologies and use-cases
  I am currently running MIRA with.
</para>
<para>
  Nothing is perfect, and both MIRA and this documentation (even if it is
  rather pompously called <emphasis>Definitive Guide</emphasis>) are far from
  it. If you spot an error either in MIRA or this manual, feel free to report
  it. Or, even better, correct it if you can. At least with the manual files
  it should be easy: they're basically just some decorated text files.
</para>
<para>
  I hope that MIRA will be as useful to you as it has been to me. Have a lot
  of fun with it.
</para>
<para>
  Burlington, Spring 2016
</para>
<para>
  Bastien Chevreux
</para>
</preface>
