I can't help with the cfasta conversion, but I can with the annotation portion. There are basically two types of annotation that you might be referring to de novo or variant annotation. I'll try and describe both.

If this is a newly sequenced organism and you are doing de novo annotation (i.e no existing reference genome), you can use MAKER for structural annotation as well as MAKER and InterProScan for functional annotation. Also look at gmod.org for other annotation tools from the generic model organism database project.

If this is a human genome (or an organism with an existing reference genome), and you want to annotate functional variants, use BWA to align to the reference, GATK or samtools to identify and variants (SNPs and indels). Then use VAAST or annonovar to classify and prioritize the variants.

Also, to follow up on Carson's reply if this is ABI data for a novel genome and you're hoping to annotate the genome, you'll need to assemble it some how first. There are plenty of tools out there for this sort of task, and which one you choose will depend on a number of factors. Google will lead you to plenty of discussion - I'd have a look at Abyss (http://www.bcgsc.ca/platform/bioinfo/software/abyss) and then read a few threads like this (http://seqanswers.com/forums/archive/index.php/t-1424.html) to get a flavor for some of the issues involved. Coming from CS you'll feel right at home with all the technical details of the De Bruijn and Euler graphs involved in these tools - it's fun stuff!

Hey,

if you have data, where the filename is like "_F3.csfasta" there should be a corresponding "_F3.qual" file. Both files together are your reads, coming out the sequencer. Now, depending on which sequencing plattform has been used, you have "create/apply" your "pipeline". In the case that you are working on a whole genome project, the data should be whole genome seq.. The infix F3.xxx is meaning that these are single end reads, paired end would be R3.xxx.

First of all you should search for a pipeline, with the attributes of single end reads, your seq plattform and whole genome seq. You will find some ;)

So the steps would be:

• Map your data to a reference (search for "hg18" or "hg19", human genome - 19 is newer) using maybe BWA
• Call your SNPs, GATK or samtools
• Annotate your SNPs, this is, also like the mapping, a science by itself. ATM I am using NGS-SNP.

These are the real basic steps.

I've not had to mess around with colour space data before, but I'm pretty sure that the the instrument manufacturers ABI share software to do that sort of conversion. The software is Corona-lite which can be downloaded from here.

You'll need to register with ABI, but I think it's free.