Re: [wgs-assembler-users] meryl crashing on large fastq input

[Brian W. <th...@gm...>]

On Wed, Apr 29, 2015 at 5:41 PM, mathog <ma...@ca...> wrote:

> On 29-Apr-2015 14:19, Brian Walenz wrote:
>
>> Plus, the assembler does completely ignore
>> the name, getting pairing from ordering in the fastq.
>>
>
> So I take it one should not apply any filtering to the Illumina data
> before entering it into CA that would cause the fastq files to get out of
> sync?
>

Yeah, that'd be bad.  Probably worse than giving the same file name twice,
which I've done before.  IIRC, the assembly wasn't total garbage, but had
bizarre stats in the QC report.

The original read names are stashed in *.gkpStore.fastqUIDmap, one line per
mate pair, if you want to check previous assemblies.

b