[Bioperl-l] Aligning Reads

[Sean Davis]

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.

Sean