Wednesday, April 6, 2011

novoalign without "-k"(left) and with "-k" (right)

# Hash length: 13 # Hash length: 13
# Step size: 1 # Step size: 1
# Paired Reads: 96409627 # Paired Reads: 96409627
# Pairs Aligned: 62936012 # Pairs Aligned: 62971552
# Read Sequences: 192819254 # Read Sequences: 192819254
# Aligned: 128634931 # Aligned: 128720259
# Unique Alignment: 126260501 # Unique Alignment: 126343058
# Gapped Alignment: 2033737 # Gapped Alignment: 2039288
# Quality Filter: 1530071 # Quality Filter: 1530624
# Homopolymer Filter: 48808 # Homopolymer Filter: 48964
# Elapsed Time: 9737.411 (sec.) # Elapsed Time: 10373.065 (sec.)
# CPU Time: 3654.4 (min.) # CPU Time: 3922.4 (min.)
# Fragment Length Distribution # Fragment Length Distribution

1 comment:

  1. Benefit of -k varies a lot between runs and it also helps larger genomes more than small genomes. Another way to test the benefit of -k is to look at quality of SNP calls and concordance with dbSNP. On 20-30X read depth it can make a significant improvement in specificity for SNPs.

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