HISAT Pipeline (http://www.ccb.jhu.edu/software/hisat/manual.shtml)
(1).Indexing a reference genome

$hisat-build  /reference/mouse/mm9.fa  /reference/mouse/mm9

#The command should print many lines of output then quit. When the command

completes, the directory will contain ten new files that all start with

`mm9` and end with `.1.bt2`, `.2.bt2`, `.3.bt2`, `.4.bt2`, `.5.bt2`, `.6.bt2`,

`.rev.1.bt2`, `.rev.2.bt2`, `.rev.5.bt2`, and `.rev.6.bt2`.  These files constitute the index - you're done!

(2).Aligning reads

$hisat  -X  /reference/mouse/mm9  -1  /Data/reads_1.fq  -2  /Data/reads_2.fq  -S  reads.sam

(3).Use `samtools view` to convert the SAM file into a BAM file

$samtools  view  -bS  reads.sam  >  reads.bam

(4).Use `samtools sort` to convert the BAM file to a sorted BAM file

$samtools  sort  reads.bam  reads.sorted

# We now have a sorted BAM file called `reads.sorted.bam`. Sorted BAM is a useful

format because the alignments are (a) compressed, which is convenient for

long-term storage, and (b) sorted, which is conveneint for variant discovery.

References:
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1.HISAT: a fast spliced aligner with low memory requirements