Hi,
As I promised in another thread here some first controlled benchmarks from the Genomatix Mapping Station ( GMS):
Mapping time: 375 seconds
Correctly identified reads: 921.799 (92 %)
Found perfect alignment for read with indel: 2.653 (0.2%)
Ignored because ambiguous: 43.057 (4%)
=====================================
Real life data:
Illumina: ChipSeq STAT1 human
Total: 5.069.935 reads
Length of reads: 36
Time: 1.524 sec (about 5 min per 1.000.000 reads)
Result:
4.150.890 unique best hits (81 %)
3.151.593 with alignment score > 0.9
207.636 of the unique hits with alignment score > 0.9 have at least on insertion or deletion in the alignment
560.920 reads with multiple best hits
====================================
Real life data:
Helicos DGE human tissue
Total: 4.397.276 reads
Length of reads: 5bps to 140bps
Time: 527 sec
Result:
1.662.837 sequences were ignored (too small) (37 %)
2.011.375 unique best hits (45 %)
777.434 with alignment score > 0.9
665.631 of the unique hits with alignment score > 0.9 have at least on insertion or deletion in the alignment
723.064 reads with multiple best hits
As I promised in another thread here some first controlled benchmarks from the Genomatix Mapping Station ( GMS):
- Random pick of 1Mio reads (32bps) across the human genome (NCBI build 36)
- Generate 1bps insertions and 1bps deletions in 1% of the reads
- Generate 1 bps substitutions in 10% of the reads
Mapping time: 375 seconds
Correctly identified reads: 921.799 (92 %)
Found perfect alignment for read with indel: 2.653 (0.2%)
Ignored because ambiguous: 43.057 (4%)
=====================================
Real life data:
Illumina: ChipSeq STAT1 human
Total: 5.069.935 reads
Length of reads: 36
Time: 1.524 sec (about 5 min per 1.000.000 reads)
Result:
4.150.890 unique best hits (81 %)
3.151.593 with alignment score > 0.9
207.636 of the unique hits with alignment score > 0.9 have at least on insertion or deletion in the alignment
560.920 reads with multiple best hits
====================================
Real life data:
Helicos DGE human tissue
Total: 4.397.276 reads
Length of reads: 5bps to 140bps
Time: 527 sec
Result:
1.662.837 sequences were ignored (too small) (37 %)
2.011.375 unique best hits (45 %)
777.434 with alignment score > 0.9
665.631 of the unique hits with alignment score > 0.9 have at least on insertion or deletion in the alignment
723.064 reads with multiple best hits
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