[Bioperl-l] Aligning Reads

Sean Davis sdavis2 at mail.nih.gov
Fri Feb 5 14:40:05 EST 2010

On Fri, Feb 5, 2010 at 2:21 PM, shalu sharma <sharmashalu.bio at gmail.com> wrote:
> Hi All,
>            Is there any program available which can align reads (200-400bp
> in fasta format) against a reference sequence and the whole alignment can be
> viewed graphically.
> I tried bowtie but i think it only takes fastaq format.

Take a look at the -f option for bowtie.


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