File: Complete assembly flow

Here is a description of what to do to get an ALLPATHS assembly from
Solexa data.

The program <Assemblez> runs the whole assembly flow from start to
end.
Here is a description by parts:

Run <SolexaToAllpaths> to take a <Solexa pipeline output dir> and
create from it an <ALLPATHS project dir>.  The latter includes
the reads, the read qualities, pairing information for paired reads.
SolexaToAllpaths also does some initial <read filtering>.

For simulated date, instead of the above, you would run
<SeqToPaths> with arguments that tell it to create simulated reads
from the reference genome.

Run <FindStrongKmers> to identify strong kmers.  Then use that for
error correction.  Run <ProvisionalEdits> to do error correction.

Run <ReadsToPaths> to create <kmer numbers> and convert each corrected
read to a <kmer path>.  

Run <RemoveSuspiciousReads> to remove suspicious reads.

Run <Unipather> to find unipaths in kmer space.

(Sanity check: run <UnipathEval> to gauge how well the unipaths turned
out.)

Then <UnipathLocs> which for low-copy unipaths finds reads
that are aligned perfectly to this low-copy unipath.

Then <PathsToLocs> maps unipaths back to the reference
sequence  (for simulated data only).

Then, generate the unipath link graph.
	     contains an estimate of the distance between low-copy
	     unipaths.

Then after this run <LocalizeReads>.