I'm just wondering if anyone has any experience with AMOScmp on short reads and how they find the performance.
I'm considering using it for large scale human genome resequencing.
Best regards, Colin
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we have a couple extensions to AMOScmp specifically targeted at short read sequences. These seem to do quite well, though I don't think we've extensively tested them on human data.
The two scripts are available in Sourceforge AMOS CVS under:
When you compile AMOS, the scripts should install automatically under the bin/ directory (without the .acf extension).
The README file contains some extra information about the two scripts.
Also, note that you'll have to retrieve the tip of the CVS distribution rather than the .tar.gz file as not all changes have propagated to the official release yet. Below are the details on how to do that.
Mihai
cvs -z3 -d:pserver:anonymous@amos.cvs.sourceforge.net:/cvsroot/amos co -P AMOS
cd AMOS
./bootstrap
./configure
make
make install
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Hi Mihai,
Thanks for your reply. I've downloaded AMOS and tried AMOScmp on some Bacteria reads and the pipeline ran perfectly and quite fast.
However I had a problem viewing the results in Hawkeye as it took forever to display anything. I could display some of the shorter contigs but not the scaffolds.
I used a 4Mbp genome with 326Mbp of short reads which produced a 1.2Gbyte Bank. My workstation has 8Gbyte of RAM.
Any idea how I can improve the performance?
Thanks, Colin
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viewing Solexa data in Hawkeye currently runs into performance issues. We're trying to figure out a way to do this, however we do not have a good solution just yet.
Mihai
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Hi,
I'm just wondering if anyone has any experience with AMOScmp on short reads and how they find the performance.
I'm considering using it for large scale human genome resequencing.
Best regards, Colin
Colin,
we have a couple extensions to AMOScmp specifically targeted at short read sequences. These seem to do quite well, though I don't think we've extensively tested them on human data.
The two scripts are available in Sourceforge AMOS CVS under:
src/Pipeline/AMOScmp-shortReads-alignmentTrimmed.acf
src/Pipeline/AMOScmp.acf
When you compile AMOS, the scripts should install automatically under the bin/ directory (without the .acf extension).
The README file contains some extra information about the two scripts.
Also, note that you'll have to retrieve the tip of the CVS distribution rather than the .tar.gz file as not all changes have propagated to the official release yet. Below are the details on how to do that.
Mihai
cvs -z3 -d:pserver:anonymous@amos.cvs.sourceforge.net:/cvsroot/amos co -P AMOS
cd AMOS
./bootstrap
./configure
make
make install
Hi Mihai,
Thanks for your reply. I've downloaded AMOS and tried AMOScmp on some Bacteria reads and the pipeline ran perfectly and quite fast.
However I had a problem viewing the results in Hawkeye as it took forever to display anything. I could display some of the shorter contigs but not the scaffolds.
I used a 4Mbp genome with 326Mbp of short reads which produced a 1.2Gbyte Bank. My workstation has 8Gbyte of RAM.
Any idea how I can improve the performance?
Thanks, Colin
Colin,
viewing Solexa data in Hawkeye currently runs into performance issues. We're trying to figure out a way to do this, however we do not have a good solution just yet.
Mihai