# How to Ray with 454 reads

For single reads, just use

mpirun -np 9999 Ray \
-s HFIEHFUE.sff -s KFKOEOKFE.sff


For paired reads, you must extract manually the reads.


convert-sff.sh is available at https://github.com/sebhtml/454-pairs

It utilises ssf_extract to get reads from the sff file.
Then, it create 3 files:

	outputPrefix.Reverse.fastq
	outputPrefix.Forward.fastq

and

	outputPrefix.Single.fastq

The 2 first should have the same number of entries.



To give them to Ray:

mpirun -np 133 \
-p outputPrefix.Reverse.fastq outputPrefix.Forward.fastq \
-s outputPrefix.Single.fastq