A Speedy Introduction to Sequence Analysis in the CloudΒΆ


  1. Start by Renting a computer from Amazon.

    (Be sure to go through Installing your Amazon EC2 system.)

  2. Now, go through the instructions in UNIX, ssh, and scp; you can skip the introduction and go straight to either Using SSH/SCP on Windows or Using SSH/SCP on Mac OS X in the Terminal app.

  3. You should now be able to log into your EC2 machine!

  4. Now, work through Running BLASTs on UNIX.

    And voila! You’ve done sequence analysis on the cloud!

  5. Let’s do some next-gen stuff – try out Mapping with bowtie.

  6. Once you’re done with that, you can also try Visualizing mappings with Samtools.

  7. And, finally, assembly! See Short Read Assembly.

Don’t forget to shut down your machine when you’re all done... You can do this by typing

%% shutdown -h now

but you will lose all of your data if you don’t transfer them off using scp (see UNIX, ssh, and scp). To see about retaining data in an EC2-accessible form, visit Storing data persistently with Amazon.

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