Page Comparison

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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.

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

1. Run

   Code Block
   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

      Code Block
      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 do use the -consed option with Newbler, follow the instructions in README_consed.txt to re-format it's output for use wiht consed (this isn't perfect...)