This demo demonstrates the usage of 

    miraEST
    convert_project

to perform an EST assembly and SNP analysis.

To run the demo, just execute 'runme.sh'.

step1_* files are mostly not of interest, so I won't describe them
here. 

step2 files are named after the strain or organism they belong
to (in this case "strain1_*" and "strain2_"). The results in these
files represent the clean transcripts collected in one strain or
organism and then assembled by miraEST.

Files in step3_* files show the last step of a complete EST transcript
analysis: determining and categorizing SNPs in closely related clean
transcripts.

Once finished, to examine the detected SNPs you can look at the html
file 'step3_out.html' using a CSS compliant browser. You can also use
the gap4 program: change into the 'step3_out.gap4da' directory, start
gap4, make a new project, import the project as directed assembly
(file of filenames is named 'fofn'). Be sure to have included the
provided extension to the GTAGDB file, so that you can switch on
display of the PAOS, PROS and PIOS tags

The type of tag depends on the strain sequences that went into that sequence
