mapping tool for short and long reads

[doublealice]

Hi,

Please forgive if this had been asked before.

I need one tool to map illumina short paired end reads (150bp) and Pacbio long reads to a genome. Usually I used bowtie2 for short reads, and blasr for Pacbio reads. But I have no idea if there is one tool work for both type of data.

I found one paper used blat but can blat handle paired-end reads? Please give some suggestions. Thanks!

[Michael.Ante]

I'm sure bbmap can do that.
STAR works very well with Illumina reads and the guys from Pacific Bioscience did some parameter optimisation to have it also working for PacBio reads (see here).

Cheers,

Michael

[GenoMax]

bwa mem also works with both short and long reads.

[doublealice]

Thanks Michael and Genomax. I will try both.