Phred, Phrap, Consed, cross_match, daev

The "conventional" sequencing tools Phred, Phrap, and Consed along with their helper programs are installed on Fourierseq.

Phred is version 0.020425.c
Phrap is version 1.080812
Consed is version 20.

All documentation is on fourierseq in: /usr/local/genome - consed in particular is only documented in a lengthy text document called "README_consed.txt". It has wonderful examples - please go through them before trying your own assembly project.

All the example data is stored in /opt/consed20 - make a local copy for your own training and testing.

To run on an ace file from Mira or Newbler - there are two ways to get the assembly to open in consed:

Run
```
consed -nophd -ace <file.ace>
```
or
1. create a directory and name it with your project name (test_consed, for example)
2. In that test_consed directory, create the following directories (Exact naming) :
  chromat_dir
  edit_dir
  phdball_dir
  phd_dir
  sff_file
3. Go into the edit_dir directory and place the 454Contigs.ace file in there. Run consed from this location by just typing
```
consed
```
4. When the screen pops up, it'll show a listing of the ace files and the contigs, choose one and open.

BUT you can't use many consed features unless you either run Newbler with the -consed option. We currently don't have a good option for converting Mira output cleanly to consed - SPHS hasn't researched this enough... any user solutions out there?

If you did use -consed, here are the quick notes from the README_consed.txt file:

9.78)  USING 454'S NEWBLER ON YOUR OWN DATA

First you should run through the tutorial above so that you know
that everything works with my test dataset.

9.79)  Run Newbler according to the 454 documentation using the -consed
option.

9.80)  Delete the .consedrc file that Newbler creates in edit_dir--it is
intended for obsolete versions of consed and may cause problems with
the current version.

9.81)  Delete the phd.ball link in edit_dir--it is also intended for
obsolete versions of consed and may cause problems with the current
version.

9.82)  Check that the current version of sff2scf is the one to be used.

Type "sff2scf -v"
It should say "080714".  If instead it says
       "Error:  Unable to open SCF file:  ../chromat_dir/-v",
your version is old and should be discarded.  Use the new version that
comes with consed.