Who is the best way to align/assemble to a reference?

[anyone1985]

There are so many software to mapping the solexa/SOLid reads to reference. Which is the best?

[francesco.vezzi]

There are so many software to mapping the solexa/SOLid reads to reference. Which is the best?

If you wont to align against a reference sequence more or less all the software are pretty good. They differ a bit from what concern speed and sensitivity but more or less are similar. In my lab we use our own tool that is more sensitive then ELAND and it has performances similar to BOWTIE an SOAP.

For what concern assembly the best software is VELVET. I use also EULER-SR that is some cases perform better then VELVET.
Also EDANA is pretty good but VELVET and EULER are better...

[nilshomer]

There are so many software to mapping the solexa/SOLid reads to reference. Which is the best?

As a biased alignment tool author, I would suggest BFAST for indels and sensitivity.

https://secure.genome.ucla.edu/index.php/BFAST

[anyone1985]

Thanks. When I assembled my data, I found the velvet was pretty good. And, I also tried to extend the sequences by different aligment. I would like to find more software with various ideas to help me finish my genome.

If you wont to align against a reference sequence more or less all the software are pretty good. They differ a bit from what concern speed and sensitivity but more or less are similar. In my lab we use our own tool that is more sensitive then ELAND and it has performances similar to BOWTIE an SOAP.

For what concern assembly the best software is VELVET. I use also EULER-SR that is some cases perform better then VELVET.
Also EDANA is pretty good but VELVET and EULER are better...