TIGR ASSEMBLER V2.0
~~~~~~~~~~~~~~~~~~~
TIGR Assembler is a program that builds a consensus sequences from
smaller nucleotide sequences.  Input is given as .seq sequence FASTA
files and .qual quality value(1) files.  See the 'data/201.pre' 
directory for an example of the input files and 'data/201.post' for
example output files.

This file contains:
. FILE CONTENTS
. PREREQUISITES
. INSTRUCTIONS
. LIMITATIONS
. NOTES


FILE CONTENTS
-------------

This is the software root directory for the TIGR_Assembler_v2
source code.

LICENSE   This is the artistic, open source license accompanying TIGR Assembler.
COPYRIGHT The TIGR copyright notice accompanies all software releases.
README    This file is at the top level.
bin/      The executables directory; binaries are placed here after
	  compilation.
obj/      Object files are placed here during compilation.
data/     Sample data directory.
src/      Software source and Makefile are here.


PREREQUISITES
-------------
TIGR ASSEMBLER needs the following to run:

1) a UN*X or Linux based machine with 32 or more MB of RAM; this requirement
   varies with the data set size being assembled
2) a C compiler capable of compiling both K+R C and ANSI C
3) /bin/csh (C shell); for the launcher


INSTRUCTIONS
------------
A.  This software must be compiled before use.  To compile this software, do 
    the following:

   1) Change into the src directory.

      cd src

   2) Build the TIGR Assembler

      make

B.  To use the software, add the TIGR Assembler and its run_TA launcher to 
    your program path.  To do this, use the following steps.

   1) Change into the software root directory (ie. you should see "bin", 
      "src", "data", "obj", and "README" in a file listing).

   2) Add the "bin" directory to your path.

      setenv PATH `pwd`/bin:${PATH}

C.  To test the software, use the data in the "data" directory.

   1) Change into the data directory, pre-run template.

      cd data/201.pre

   2) Run the TIGR Assembler on the data.  Note, you must have run_TA and
      TIGR_Assembler in your path.  See the instructions in Section B above.

      run_TA "-s -q 201.qual -C 201.contigs" 201.seq

   3) Compare the results of the 201.pre directory with the 201.post directory.

      cd ..  # move out of the 201.pre directory
      diff -r 201.pre 201.post


LIMITATIONS
-----------
.  Input sequences must be less than 1000 base pairs each (approximately).
.  There may be up to 17 quality values per line in the .qual file.  That is,
   every line but the last line for an input sequence must have 17 quality
   values.
.  The maximum number of input sequences is limited to 524,000 approximately,
   less depending on input sequence size and machine memory.


NOTES
-----

1) Information on quality values is available from
   http://www.phrap.org/ .  The scheme implemented there is used by
   TIGR Assembler.


TIGR Closure Software Group
04/21/2003