Daniel:Notebook/GenomeMiner/2013-10-9
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HL155 Novoalign (Started 10/3/2013)[edit]
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%