Coffee bacs

Location:

 /fs/szasmg2/coffee/

BACS:

CA1A
CA1B

Best assemblies:

CA1A : CA3, genomeLen=100K 
CA1B : CA4

CA1A:

  * The  CA_24Sept07 assembly had a 15KB long degenerate. This
    degenerate has high coverage (~ twice the average) and high GC%
    (41% vs avg of 36%). There are no correlated SNP's in it and no
    missoriented mates so it is probably not a collapsed repeat. I
    wonder if due to its high GC this area in the BAC might have got
    cloned preferentially.The degenerate has several links to placed
    contigs.
  * A new assembly run by setting the assembly size to 100K managed to
    incorporate the previous degenerate into its longest scaffold.
    This assembly is located under
    /fs/szasmg2/coffee/CA1A.inputs/CA_04Oct07-CA3-100K/
  * Several scaffolds are linked to other scaffolds by single mate
    pair links. CA needs at least 2 mate pairs in order to link
    contigs together.
  * Bambus, run with redundancy=1 resulted in 10 scaffolds, but not
    all are linear . The Bambus files are located under
    /fs/szasmg2/coffee/CA1A.inputs/CA_04Oct07-CA3-100K/bambus/
  * Celera Assembler version 4 (CA4) did not perform any better than
    CA3.11
  * autoJoiner did not close any sequence gaps

CA1B:

  * The CA4 assembly closed one sequence gap from the CA_24Sept07
    assembly. The CA4 assembly is located under
    /fs/szasmg2/coffee/CA1B.inputs/CA_04Oct07-CA4/
  * autoJoiner did not close any sequence gaps