Hi, I'm new to bioconductor. After looking at the package descriptions, and FAQ, it was not obvious to me how to do these tasks:

1. Read ABI-format DNA sequence chromatograms, and then print them nicely (e.g, PDF or PS, with called bases, multiple lines/page)
2. Export sequence data from #1 (e.g., FASTA, etc)
3. Assemble ~10 such reads (from #2) into a consensus sequence (my reads typically cover a plasmid insert, ~1,500 bases total)
4. Do all of the above in Linux, from the command line (i.e., batch processing).

I've looked into phred/phrap...but they would cost >=$10K, not reasonable for our occasional need (~6 times/year). Also had a look at Staden/Trev, and FinchTv, both of which seem to not support command line and/or batch processing (and FinchTv doesn't assemble).

Am I missing the obvious bioconductor package? Any other suggestions? Thanks very much!

 

David Borhani
Please respond to: david.borhani@alum.mit.edu
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