[BioC] alignment & SNP calling

[Daniel.Berner at unibas.ch]

Dear list
1) I have illumina short reads from which I want to call SNPs WITHOUT  
using a reference genome. That is, I want to align the reads among  
themselves, and then screen each alignment for polymorph positions  
(SNPs) by taking into account base call quality. Is there a program  
that would allow building such alignments without reference genome,  
and that produces output that can be input to R/bioconductor?
  2) Generally, are there R/Bioc implementations for SNP-detection  
using base-call quality?
Daniel Berner