SOLID data processing by using BFast

[david.tamborero]

Hello,

I am beginning in the NGS processing world, and I have to deal with SOLID reads. I have carefully read the manual and supplement data papers of both BWA and Bfast but I still have some doubts:

- We use 50 bp single-paired and 25 bs mate-paired reads. I will use Bfast with the recommended arguments for the former scenario, but can someone suggest me which is the best option for the second one?

It is well explained , but I still don't get the point of using several indexes in Bfast. I suppose that it should give more sensitivity for searching variants, but can someone tell me whether to use several masks is always mandatory?

I really appreciate your help, sorry for my ignorance!

David

[epigen]

The BFAST developers recommend to use bfast bwaaln for 25 (35) bp reads. But 25+25 bp is really really short, I thought the mate-pair standard is 50+50 whereas for paired-end it's 50+35 (I work with the latter).

What do you mean by "50 bp single-paired"? Reads are either single or paired.

Using several BFAST masks indeed gives more sensitivity but it is not mandatory, you can use the -i option to select a subset of indexes.

[Venkat]

How efficient is the alignment of Bfast + BWA in terms of accuracy and performance??