LAST: Genome-Scale Sequence Comparison
======================================

LAST finds similar regions between sequences, and aligns them.  LAST
is similar to BLAST, but it copes better with giga-scale biological
sequences.  It can also use sequence quality data, and it can indicate
the ambiguity of each column in an alignment.

Requirements
------------

To handle mammalian genomes, it's best if you have at least 10-20
gigabytes of real memory, but you can get by with 2 gigabytes.

To install the software, you need a C++ compiler.  On Linux, you might
need to install a package called "g++".  On Mac, you might need to
install command-line developer tools.  On Windows, you might need to
install Cygwin.

Setup
-----

Using the command line, go into the top-level LAST directory.  To
install the programs into your personal "bin" directory, use this
command:

  make install bindir=~/bin

You might have to log out and back in before your computer recognizes
the newly-installed programs.  To install them in
some/other/directory, do this:

  make install bindir=some/other/directory

To compile the programs in-place (without installing them elsewhere):

  make

If you have administrator permissions, you can install them in the
standard /usr/local/bin directory, like this:

  sudo make install

Miscellaneous
-------------

For usage instructions, please see the doc directory, especially
last-tutorial.txt.

LAST (including the scripts) is distributed under the GNU General
Public License, either version 3 of the License, or (at your option)
any later version.  For details, see COPYING.txt.

LAST includes public domain code kindly provided by Yi-Kuo Yu and
Stephen Altschul at the NCBI.

If you have any questions, comments, or problems, please email:
last (ATmark) cbrc (dot) jp.
If reporting a problem, please describe exactly how to trigger it.

References
----------

If you would like to understand LAST in detail, please look at these
articles.  If you use LAST in your research, please cite one (or more)
of them.

The main algorithms used by LAST:
  Adaptive seeds tame genomic sequence comparison
  SM Kielbasa, R Wan, K Sato, P Horton, MC Frith: Genome Research 2011 21:487.

How LAST uses sequence quality data:
  Incorporating sequence quality data into alignment improves DNA read mapping
  MC Frith, R Wan, P Horton: Nucleic Acids Research 2010 38(7):e100.

Choice of score parameters, ambiguity of alignment columns, and
gamma-centroid alignment:
  Parameters for Accurate Genome Alignment
  MC Frith, M Hamada, P Horton: BMC Bioinformatics 2010 11:80.
