Burrows-Wheeler Aligners for Colorspace?

[lgoff]

Does anyone know if any of the newer BWT aligners work for native ABI reads yet? I am drooling over the speed improvements, but need something to work in colorspace...Thanks in advance.

-Loyal

[doxologist]

I whole heartedly second this motion!

[lh3]

Actually you would not get much speed up from BWT-based aligners, at least not from bwa. BWT based algorithm is mainly fast for near exact alignment, but as at present SOLiD produces higher color error rate than Illumina, the advantage of BWT based algorithm is degraded. Furthermore, SOLiD reads are short in general and thus tend to have more alternative mappings. Pairing multiple hits in the BWT framework is expensive.

An experimental version of BWA now supports SOLiD pairing, but it is only 2-3 times faster than MAQ while less sensitive. For reads with high error rate, Eland/MAQ/ZOOM like algorithms may be preferred sometimes.

[doxologist]

thanks for the info.

[lh3]

bwa-0.4.6 is just released with SOLiD support. Features include: a) indexing nucleotide fasta (maq takes color reference fasta as input). b) paired end support. However, as SOLiD reads are shorter, it is recommended to tune the default parameters to achieve better speed (see manual in the package). c) output alignment in the nucleotide space (this is done by a similar algorithm implemented in maq's csmap2nt). d) gapped alignment for single end read (not sure if it works properly yet, but I can see gapped alignments). Please note like maq, bwa cannot use the primer base and the first color, which will make the read 1 residue shorter.

For SOLiD reads, bwa is not much faster than maq and less sensitive, but you may find it is easier to use. Anyway, an experimental version. Let me know if you have any problems. I seldom work with SOLiD data.

[doxologist]

Thanks for the info. To be doubly sure... By "color reference fasta", do you mean that you translate the tags from colorspace to FASTA FIRST and then do the matching? Or is the matching done in native colorspace?

[lh3]

Alignment is done in color space. After alignment, color reads are translated to nucleotides essentially with the code in maq's csmap2nt.

[doxologist]

thanks... that's what I expected... just wanted to be doubly sure.

[BioWizard]

If you're looking for the fastest colorspace alignemnt,
check out the thread:

"Alignment Software breaks speed records "

[nilshomer]

Also check out http://genome.ucla.edu/bfast for the alignment software BFAST. Higher error reads is not a problem, handling color space data easily.

Also consider what you are looking for. If you wan to find indels (gapped alignment) you will need to perform some type of smith-waterman algorithm, which is more expensive on ABI data.