File	Date	Author	Commit
build	2014-12-04	Andy Thomason	[1a2567] deleted old classes, starting to get hit result...
doc	2014-09-18	Andy Thomason	[32aecb] docs updates
examples	2014-09-18	Andy Thomason	[32aecb] docs updates
lib	2014-05-20	andy_thomason	[dc588f] opengl stub, match score selection
src	2014-12-04	Andy Thomason	[1a2567] deleted old classes, starting to get hit result...
.gitignore	2014-08-11	andy_thomason	[8d1d38] removed test dir, added stub zip lib, fixed fq ...
Makefile	2014-11-20	Andy Thomason	[3b50ac] Mac changes
README	2014-08-22	Andy Thomason	[6623f3] fixed hit buffer overflow at expense of file size

Read Me

***********************************************************************************

                                ROSALIND TOOLS

Prototype for a simple sort-based gene sequence aligner.

On all platforms:

Build using the makefile.

On Windows, use vcvars64_amd.bat to set environment variables
before building. This file comes with your visual studio in
Program Files. 

Altrnatively, on Windows, use the VC2012 solution provided to 
rosalind-align.cpp


To run:

bin/rosalind-align 1.fq.gz 2.fq.gz ref.fa.gz -o results.sam

For large runs, we suggest the following options on a 16GB machine:

--seed-buffer-size=10000 --read-chunk-size=32000000 --reverse-ref --percent-seeds=12

The seed buffer size depends on memory. You can experiment with the read chunk
size. Larger settings increase performance providing memory is available but will
reduce performance if memory runs out.

Always use a SSD! Mechanical hard drives are obsolete.