Question: What'S The Best Reads Aligner For 454 Data Now???
1
gravatar for chrislovingfreedom
6.7 years ago by
chrislovingfreedom10 wrote:

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.

alignment 454 • 2.5k views
ADD COMMENTlink modified 4.5 years ago by Biostar ♦♦ 20 • written 6.7 years ago by chrislovingfreedom10
1
gravatar for Vikas Bansal
6.7 years ago by
Vikas Bansal2.3k
Berlin, Germany
Vikas Bansal2.3k wrote:

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?

ADD COMMENTlink written 6.7 years ago by Vikas Bansal2.3k

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??

ADD REPLYlink written 6.7 years ago by chrislovingfreedom10

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.

ADD REPLYlink written 6.7 years ago by Vikas Bansal2.3k

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

ADD REPLYlink written 6.7 years ago by chrislovingfreedom10
0
gravatar for David Langenberger
6.7 years ago by
Deutschland
David Langenberger8.7k wrote:

I would recommend to use segemehl.

ADD COMMENTlink written 6.7 years ago by David Langenberger8.7k

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.

ADD REPLYlink written 6.7 years ago by Vikas Bansal2.3k

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.

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by David Langenberger8.7k

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

ADD REPLYlink written 6.7 years ago by chrislovingfreedom10

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. ;)

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by David Langenberger8.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1150 users visited in the last hour