Editing assembly output of amos?
Hello Everyone,
I hope for the love of god that someone might be able to point me in the right direction.
Essentially, I have been having trouble finding some kind of program that will allow me to edit an assembly produced by an amos assembler (specifically: AMOScmp-shortReads-alignmentTrimmed). What I am looking for is something similar to the Hawkeye visualization tool, however with the ability to make alignment edits and corrections.
Right now, we are taking the *.contig files, converting them to fasta formatted files (1 reference, multiple reads) and working with them in some kind of text editor, which is a bit of a pain as we lose all quality information.
Is consed the way to go, here? i.e., create and .ace file and load it up?
The primary goal is to tune up the assembly a bit then start looking for "high confidence" SNPs.
The collective wisdom of the SEQanswers community is most appreciated.
Thank you,
dalesan
I hope for the love of god that someone might be able to point me in the right direction.
Essentially, I have been having trouble finding some kind of program that will allow me to edit an assembly produced by an amos assembler (specifically: AMOScmp-shortReads-alignmentTrimmed). What I am looking for is something similar to the Hawkeye visualization tool, however with the ability to make alignment edits and corrections.
Right now, we are taking the *.contig files, converting them to fasta formatted files (1 reference, multiple reads) and working with them in some kind of text editor, which is a bit of a pain as we lose all quality information.
Is consed the way to go, here? i.e., create and .ace file and load it up?
The primary goal is to tune up the assembly a bit then start looking for "high confidence" SNPs.
The collective wisdom of the SEQanswers community is most appreciated.
Thank you,
dalesan
