[AMOS-help] AMOScmp aligner

[Jose B. <jb...@bt...>]

Hi:
I want to align 454, sanger and solexa reads to a reference transcriptome. I'm 
thinking on using AMOScmp. I've done some tests and I think that the nucmer 
aligner could not be the best option for some reads.
I'm thinking on using other aligner than nucmer (like bwa or bfast) and 
transforming its output into something similar to the nucmer delta file. I 
would use the AMOScmp pipeline with that modification. Do you think that's a 
sensible approach? Are there other compatible aligners with AMOScmp?
Thanks for your help.
Best regards,

-- 
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)