[Bioperl-l] Aligning Reads

[Abhishek Pratap]

I would also try Mosaik. It can take fasta as input and align both
short and long reads.

-Abhi

On Fri, Feb 5, 2010 at 2:40 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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
>
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