You won't be able to run bwa on windows directly unless you use cygwin or a virtual linux machine.
But before you get to that save yourself trouble and find new computer with 64-bit OS. 32-bit windows is going to pose a problem at some point soon where you are going to run into memory limit (that could be because of the size of your dataset or the size of the genome (e.g. human) you are working on).
If you are set on using your computer as is then look at BBMap suite (and BBDuk - trimming and BBMap - alignment) programs.http://seqanswers.com/forums/showthread.php?t=41057 They are native java programs and will run on windows directly. They will still be subject to above memory limits.
But before you get to that save yourself trouble and find new computer with 64-bit OS. 32-bit windows is going to pose a problem at some point soon where you are going to run into memory limit (that could be because of the size of your dataset or the size of the genome (e.g. human) you are working on).
If you are set on using your computer as is then look at BBMap suite (and BBDuk - trimming and BBMap - alignment) programs.http://seqanswers.com/forums/showthread.php?t=41057 They are native java programs and will run on windows directly. They will still be subject to above memory limits.
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