aligning .sra files in colorspace with fasta reference genome

[masme]

Hello
I am currently doing an intership in bioinformatics and I am looking for a good pipeline to process abi SOLiD data coming from the NCBI sra-data repository.
The eventual goal is to perform peakcalling on an alignment coming from a colorspace fastq and a plain fasta reference genome.

I'm having trouble finding a good (working) tool to align the colorspace fastq and the fasta genome. Does anyone have any tips?

I already know it's not a good idea to convert colorspace to basespace, so I'm looking for alternatives. Bowtie and BWA don't seem to work for me...

much thanks!
masme

[mastal]

I seem to remember that BFAST was specifically written for colorspace data.

[masme]

Thx! I'm looking into BFast, but it seems to have problems with indexing my fasta genome.

"In function "BfastIndexValidateInputs": Fatal Error[IllegalFileName]. Variable/Value: mask."

I'm sure though that my fasta file is in order, the fasta2bgr module of BFast doens't throw this error..