What'S The Best Reads Aligner For 454 Data Now???

Question

[chrislovingfreedom]

Hi,@all Now, I want to align my 454 reads to refence sequence. Which tool is best recommened?? I see someone say MOSAIK. But the MOSAIK site's latest released version is on 2010-10-01. Is it outdata? And does someone could recommend a useful tool for 454 sequences?? Thx! Appreciate for your reply.

Answer 1

[Vikas Bansal]

Hi, here, I found latest release - 2011-11-08 - MOSAIK 2.1 . You can also use BWA. Here is the Biostar tutorial.

How long your reads are and what is your reference sequence?

[chrislovingfreedom]

It is yeast genome about 200bp. Do you known whether MOSAIK is still under maintenance for it has NO new release about 9 months. And the long reads aligner for 454 is BWA or BWASW??

[Vikas Bansal]

For alignment with BWA, there are two algorithms - aln (for short reads) and bwasw (for long reads). Please have a look at this manual. For MOSAIK, I found 2.1 only.

[chrislovingfreedom]

Thx for your reply. And another tool SSAHA2 seems also can be used for long reads. Do U have some suggestion?

Answer 2

[David Langenberger]

I would recommend to use segemehl.

[Vikas Bansal]

Hi. I have a question. Segemehl says short reads mapping but OP says 200bp long reads from 454 sequencing. Can we use it for long reads and could please provide little overview of advantages of segemehl.

[David Langenberger]

Of course you can use segemehl with your 454 data. Compared to BWA and other mapping tools, segemehl has similar sensitivity... perhaps slightly better, but actually not worth to mention. The main advantage over other mapping tools is the possibility to get split reads. You do not need any re-mapping step, since, based on the algorithm, segemehl can directly map reads to splitted positions (also these from fusion transcripts; very high distance; strand switches; different chromosomes). Furthermore, and there the length of 454 reads gets actually very interesting, segemehl can map multi-split reads, meaning one read, which maps to more than just two positions. I'm not sure, if you need that, but I think it's worth a try.

[chrislovingfreedom]

Thx a lot. And could you introduce the difference between Segemehl and BWASW, MOSAIK??

[David Langenberger]

I have never worked with MOSAIK, so I cannot say anything about it. BWASW I mentioned above.... not a big difference in mapping accuracy.... segemehl is perhaps slightly better. I mean.... all these tools are very fast and accurate.... in the end it comes down to the usability, I think. And there I really like segemehl, since it's a 'one-stop-shop' solution. The only drawback is the memory footprint, but it should be doable with nowadays machines. I just recommend to try it... if you like it in the end, I don't know. ;)