Re: [AMOS-help] Want to know how to use FASTQ files as AMOS input

[Lionel G. <guy...@gm...>]

Hi Vasu,

I don't know if it helps you, but there is a Biopel module that can  
parse fastq. It shouldn't be too hard to write a short script to  
translate fastq into fasta and qual

Lionel

On 23 Mar 2009, at 16:24 , Adam Phillippy wrote:

> Hello Vasu,
> Currently there are no FASTQ converters included in the AMOS  
> release. You will need to convert these files manually to FASTA  
> format before you can run any of the AMOS tools.
>
> Best,
> -Adam
>
>
> On Thu, Mar 19, 2009 at 3:00 PM, Vasu Raghavan <vra...@se... 
> > wrote:
> Hello
>
>
> I have short reads in FASTQ format. I want to use AMOS to assemble  
> from this FASTQ files. Do I need to convert FASTQ files to FASTA or  
> other format before I can use AMOS pipelines like runAmos? If so,  
> can you please describe the AMOS command I should use? I tried with  
> toAmos but toAmos complains that the file starts with a weird line.
>
>
> Thanks and regards,
>
>