Examples of Mapping Color Space Sequences to 3GB Human Genome
 These results were reported to us by Applied Biosystems (Foster City), using just one
of the ISAS / GenomeCruncher (2.4GHz  8 core) systems they had purchased from us.
Run times can be faster on more powerful servers, or slower on inferior ones.
Run Description
 Total
Bases
 Total Run
Time
 Uniquely Mapped
and AAA for matepair
200 Million 25mers with 2 substitutions
 5G
    
400 Million 25mers (200M+200M matepairs)
4 substitutions per 50mer pair
 10G
 104 minutes
 61.0%
500 Million 50mers with 5 substitutions
 25G
 2.5 hours
 41.0%
1 Billion 50mers (500M+500M matepairs)
10 substitutions per 100mer pair
 50G
 7.5 hours
 33.1%
Alignment Mode
 Alignment Rate (Reads/Hour)
First rate does not include writing
SAM output file. Second rate does.
 Mapped
 Uniquely
Mapped
35mers 1 substitution
 1.81 Billion or 1.01 Billion
 94.1%
 71.8%
35mers 1 substitution, insertion, or
deletion (gapped)
      
60mers 2 subs
 905 Million or 609 Million
 90.8%
 76.1%
60mers 2 subs, ins, or dels (gapped)
      
75mers 3 subs
 511 Million or 401 Million
 89.5%
 76.2%
75mers 3 subs, ins, or dels (gapped)
      
88mers 4 subs
 352 Million or 294 Million
 84.5%
 73.6%
88mers 4 subs, ins, or dels (gapped)
      
Examples of Mapping Illumina Sequences to 3GB Human Genome
We ran data supplied by NCGR on one ISAS / GenomeCruncher (2.4GHz  8 core)