Daniel:Notebook/GenomeMiner/2013-10-9

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

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V4S3[edit]

Pipeline[edit]

Build Index

novoindex index_v4s3fullrevcomp.ndx V4S3_fullrevcomp.fa

Novoalign

novoalign -d index_v4s3fullrevcomp.ndx -f ../../s_2_1_Indx13.txt -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s3.sam


Alignment Results[edit]

#     Read Sequences: 11450664
#            Aligned:  4180484
#   Unique Alignment:  4172662
#   Gapped Alignment:  2905583
#     Quality Filter:    25772
# Homopolymer Filter:       38
#       Elapsed Time: 10011.583 (sec.)
#           CPU Time: 128.9 (min.)
# Done at Wed Oct  9 13:18:23 2013

Error Counting Results[edit]

Error Rate: 6.73%
Error Rate of Insertions: 3.26%
Error Rate of Deletions: 2.35%
Error Rate of Substitutions: 1.12%