I'm probably asking a basic question, but I've searched for hours and can't seem to find a straight answer.
We have recently sequenced the entire genome (~5 MB) of a Salmonella strain using a brand new 454 sequencer. Ours was one of the first sequences ran. Since this is new, no one here really knows what to do with the data.
I ran the sff reads through gsAssembler (i.e. Newbler) and now have contigs. There are several strains of Salmonella that have been sequenced and fully annotated. Thus, I believe it would be easiest to compare the contigs to a reference strain to figure out what gaps need to be filled. I used Gs Reference Mapper to do this, but the data that comes out of Mapper is significantly less than what comes out of Assembler. Thus, I think Mapper might be chopping up the contigs to make them fit better.
Is there a program where I can use the contigs produced from Assember (which are .ace files) and compare them to a reference sequence that I have in a .fasta format? I have access to Consed, but can't seem to add a .fasta file into Consed to use as a reference.
Thanks for the help!
We have recently sequenced the entire genome (~5 MB) of a Salmonella strain using a brand new 454 sequencer. Ours was one of the first sequences ran. Since this is new, no one here really knows what to do with the data.
I ran the sff reads through gsAssembler (i.e. Newbler) and now have contigs. There are several strains of Salmonella that have been sequenced and fully annotated. Thus, I believe it would be easiest to compare the contigs to a reference strain to figure out what gaps need to be filled. I used Gs Reference Mapper to do this, but the data that comes out of Mapper is significantly less than what comes out of Assembler. Thus, I think Mapper might be chopping up the contigs to make them fit better.
Is there a program where I can use the contigs produced from Assember (which are .ace files) and compare them to a reference sequence that I have in a .fasta format? I have access to Consed, but can't seem to add a .fasta file into Consed to use as a reference.
Thanks for the help!
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