add instances

ngs-docs · May 9, 2017 · 3d0a2ff · 3d0a2ff
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diff --git a/README.md b/README.md
@@ -8,4 +8,4 @@ These lessons were developed and tested on EC2 using Ubuntu 15.10; the
 image was ubuntu/images/hvm/ubuntu-wily-15.10-amd64-server-20160222
 (ami-05384865) on us-west (California).
 
-We ran this on t2.xlarge instances with 4 CPUs and 16 GB of RAM.
+We ran this on m4.large instances with 2 CPUs and 8 GB of RAM.
diff --git a/_static/instances.csv b/_static/instances.csv
@@ -0,0 +1,31 @@
+assembly1,ec2-13-56-18-122.us-west-1.compute.amazonaws.com
+assembly2,ec2-52-53-243-171.us-west-1.compute.amazonaws.com
+assembly3,ec2-54-193-81-223.us-west-1.compute.amazonaws.com
+assembly4,ec2-52-53-229-54.us-west-1.compute.amazonaws.com
+assembly5,ec2-54-193-92-13.us-west-1.compute.amazonaws.com
+assembly6,ec2-54-241-130-188.us-west-1.compute.amazonaws.com
+assembly7,ec2-54-215-133-121.us-west-1.compute.amazonaws.com
+assembly8,ec2-52-53-205-136.us-west-1.compute.amazonaws.com
+assembly9,ec2-54-183-181-96.us-west-1.compute.amazonaws.com
+assembly10,ec2-54-183-189-2.us-west-1.compute.amazonaws.com
+assembly11,ec2-54-193-82-141.us-west-1.compute.amazonaws.com
+assembly12,ec2-54-183-241-61.us-west-1.compute.amazonaws.com
+assembly13, ec2-54-183-241-61.us-west-1.compute.amazonaws.com
+assembly14,ec2-54-67-46-193.us-west-1.compute.amazonaws.com
+assembly15,ec2-54-183-138-225.us-west-1.compute.amazonaws.com
+assembly16,ec2-13-56-20-201.us-west-1.compute.amazonaws.com
+assembly17,ec2-54-193-105-58.us-west-1.compute.amazonaws.com
+assembly18,ec2-54-215-246-81.us-west-1.compute.amazonaws.com
+assembly19,54.193.95.126
+assembly20,13.56.14.108
+assembly21,54.67.30.13
+assembly22,13.56.16.89
+assembly23,54.67.62.225
+assembly24,52.53.228.36
+assembly25,54.215.206.121
+assembly26,54.219.182.252
+assembly27,54.215.219.200
+assembly28,54.183.111.25
+assembly29,54.183.191.2
+assembly30,54.193.109.182
+assembly31,54.153.107.1
diff --git a/how-assembly.md b/how-assembly.md
@@ -0,0 +1,28 @@
+# How assembly works
+
+See hand outs.
+
+This is shotgun sequencing of a common Mexican phrase.  Can you assemble
+the original phrase?
+
+Rules:
+
+* no googling!
+
+* work in groups of 4-6
+
+Questions:
+
+* think about strategy; how would you do this for 10x, or 100x, the data?
+
+* does this get easier, or harder, with more people in a group?
+
+* what are strategies for verifying the results?
+
+* is it helpful that the "reads" are sorted?
+
+* what is the benefit of "paired end" reads?
+
+* what is the benefit of longer reads?
+
+* how problematic are errors in the reads?
diff --git a/index.md b/index.md
@@ -10,9 +10,9 @@ Paz, Mexico, in mid-May 2017.  Our host was Ricardo Vazquez Juarez.
 
 [BLAST as an example of command line power](blast.html)
 
-Command line, workflows, and Good Enough Practice
+[Command line, workflows, and Good Enough Practice](workflows.html)
 
-How assembly works
+[How assembly works - a practical exercise](how-assembly.html)
 
 [Actually running assembly!](assemble.html)
 

diff --git a/toc.rst b/toc.rst
@@ -8,6 +8,7 @@ Put references to your files below:
 
    README
    index
+   workflows
    aws/login-shell-win
    blast
    assemble