assemble genome use mate pair library

[huily]

Dear all,

I have a simple question which confused me a long time. Before assembling genome, do I need to reverse the mate pair reads or complement reverse the mate pair reads? Thank you very much!

Huily

[westerman]

Neither. In general you simply need to tell your assembler that you have mate pairs. They are oriented in a different direction than paired-ends but I suspect that all assemblers can handle this.

[huily]

I want to use velvet to assemble, but the velveth can't handle this. I don't know how to do that.

[Brian Bushnell]

Velvet can handle paired reads fine. Can you clarify as to whether you are using a long-mate pair or normal fragment library? For example, what is the expected insert size?

[huily]

I have two normal pair end libraries with insert 260bp and one mate pair library with insert size 7000bp. Does the long paired-end have same meaning with mate paired-end?

[Brian Bushnell]

Sometimes they are used interchangeably. To be precise, I tend to refer to the short ones as "fragment libraries" and the long ones as "long mate pair (LMP) libraries".

Normally, fragment libraries are used for assembling contigs using kmers, while LMP libraries are used for scaffolding (based on mapping). I have never used Velvet for scaffolding, just contig-making. You might try a standalone scaffolder once you have contigs from Velvet.

[westerman]

Do be aware that the directionality of (at least Illumina) reads is different between Paired End and Mate Pair libraries. For this reason I would never use the terms interchangeably.

Personally I use ABySS to assemble/scaffold PE with MP and even long read libraries. It works fine for the general case -- i.e., with the many different species I work with -- but there are probably better assemblers for the specific kingdoms.

[pmiguel]

Guys, I think you are skating around the true horror of the OPs message.

One must never reverse without complementing nor complement without reversing. Those are forbidden operations. Forbidden!!

BTW Rick, Roche screwed things up (as usual) by calling their 454 mate-pair library construction method "paired end". Well, really back in pre-next gen era , "Mate pair" and "paired end" were used interchangeably. The "mate pair" BAC sub-libraries we used to make were really what we would now call "paired end". Kind of.

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Phillip