Lab 2, CMSC 828N: Comparative Assembly

For this lab, you will use the MUMmer alignment system and the AMOScmp
and minimus assemblers to assemble a set of reads that we provide.  As
preparation for this lab, you need to download and install MUMmer,
AMOScmp, and minimus.  Links to these systems can be found at
http://cbcb.umd.edu/software.  AMOScmp and minimus are both contained
in the AMOS distribution.  Installation is straightforward; just
follow the README files contained with both distributions.
Essentially you just unpack the files and then type 'configure'
followed by 'make install'. AMOScmp depends on having MUMmer available
and in your path.

Input to both AMOScmp and minimus is an "afg" file, which we have
already created for you. This file is lab02.afg, available on the
course syllabus page with this assignment.


1. Use BLAST to determine the species to use as a reference. This will
   be the same species as your target genome.  Report the name of the
   species.

2. Use minimus to create a de novo assembly of the sequences in 
   lab02.afg.  If you want to be more ambitious, you can try running
   another de novo assembler such as Celera Assembler, which can be
   found in SourceForge.  Turn in your assembly as a multi-fasta file
   containing just the contigs.

3. Use AMOScmp to assemble the sequences in lab02.afg. You should
   download the reference genome from Genbank. The result will be a
   set of contigs.  Turn in your assembly as a multi-fasta file
   containing just the contigs.

4. Using the nucmer package within MUMmer, compare your two assemblies
   to the reference genome.  
   (a) For the minimus assembly, turn in an ordered list of contig IDs, 
   indicating "for" or "rev" for each ID.  
   (b) Turn in a short, written description of the differences 
   between your minimus assembly and the reference genome.
   This should be no more than a paragraph. You should describe how
   how similar the contigs are (identical? 99% identical? other?) to 
   the reference.  Identify any mis-assemblies.
   (c) Turn in a similar short description of your AMOScmp assembly
   as compared to the reference genome.  How many gaps are there, and
   how large are they?  What is the overall identity?