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Old 12-11-2013, 05:45 PM   #1
Mike DS
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Location: München

Join Date: Dec 2013
Posts: 6
Default Hawkeye too slow to use on laptop

I've seen some passing mention of Hawkeye being too slow, and that is my current dilemma. I installed the latest AMOS (3.1.0) successfully on Mac OS X 10.6.8, and even though I have 8 Gb of RAM, I find Hawkeye very slow. It stops for long periods to load reads (my ace file is 1.9 Gb). I like the functionality of Hawkeye (I am interested in checking assembly and correcting if needed), but I cannot put up with the slow performance when I want to scan contigs.
The reason I tried Hawkeye was because Consed would not load the ace file (originally a velvet .afg file that I converted with amos2ace - but it does not work very well and gave up part way through the phd descriptions). I normally like to use consed, but I did not know how best to deal with the ace file errors, so I looked at AMOS/Hawkeye. Even Geneious would accept the ace file, so I guess Consed is being picky.
I realise that the obvious solution to increase performance is to give up on a laptop and use better hardware, but I would first like to know if others have similar issues with Hawkeye - and if so, what solutions they found, if any. I note that Gap5 is very fast, so why is Hawkeye so slow?

Regards, Mike DS

Edit: so if Hawkeye is so slow with .afg files, why can't it open BAM files? I ended up using Tablet (had to convert the .afg to a BAM file). That runs fine on my laptop (macbook pro).

Last edited by Mike DS; 12-15-2013 at 11:41 AM.
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