Daniel:Notebook/GenomeMiner/2013-10-10

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HL155 Novoalign (Started 10/3/2013)[edit]

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V4S1 (no FULLNW)[edit]

The fullnw tag on novoalign tries to align the entire read to the entire reference, a good option when we were using the shortened references, but on the full references it might cause issues (recall high error rates from Mon,Tues, and Wed.

Pipeline[edit]

Made a modified bash script to do everything for me. Bash script

Alignment Results[edit]

#     Read Sequences: 11450664
#            Aligned:  4194879
#   Unique Alignment:  4178621
#   Gapped Alignment:  3042944
#     Quality Filter:    23301
# Homopolymer Filter:       40
#       Elapsed Time: 9952.305 (sec.)
#           CPU Time: 140.8 (min.)

Error Counting Results[edit]

Error Rate: 6.63%
Error Rate of Insertions: 0.179%
Error Rate of Deletions: 2.36%
Error Rate of Substitutions: 4.09%