Thought this might be of interest.
Illumina say the latest version of the Pipeline (v1.4) has better image analysis (Firecrest). To test this claim, I analysed both ways a 70bpx2 PhiX lane from a recent standard GAII flowcell (cycle seq kit v3).
Results indeed suggest lower error rate for Pipeline 1.4 at the same time as generating 20% more data from this cluster density.
I havent yet looked to see if there is any difference in sequencing error types.
Detail below.
David
PIPELINE 1.3
153701 raw clusters/tile
108817 post filter clusters/tile
ELAND 93.39% align, error rate 1.80%
maq-0.7.1 (map -n 3)
[match_data2mapping] 21279032 out of 21755852 raw reads are mapped with
20217141 in pairs.
-- (total, isPE, mapped, paired) = (21755852, 1, 21279032, 20217141)
Error rate 0.025004
Uniquely mapping reads (MQ>30) 20375224
PIPELINE 1.4:
153682 raw clusters/tile
131772 post filter clusters/tile
ELAND: 98.14% align, error rate 1.65%
maq-0.7.1 (map -n 3)
[match_data2mapping] 25751286 out of 26342226 raw reads are mapped with
24449419 in pairs.
-- (total, isPE, mapped, paired) = (26342226, 1, 25751286, 24449419)
Error rate 0.021450
Uniquely mapping reads (MQ>30) 24698897
Illumina say the latest version of the Pipeline (v1.4) has better image analysis (Firecrest). To test this claim, I analysed both ways a 70bpx2 PhiX lane from a recent standard GAII flowcell (cycle seq kit v3).
Results indeed suggest lower error rate for Pipeline 1.4 at the same time as generating 20% more data from this cluster density.
I havent yet looked to see if there is any difference in sequencing error types.
Detail below.
David
PIPELINE 1.3
153701 raw clusters/tile
108817 post filter clusters/tile
ELAND 93.39% align, error rate 1.80%
maq-0.7.1 (map -n 3)
[match_data2mapping] 21279032 out of 21755852 raw reads are mapped with
20217141 in pairs.
-- (total, isPE, mapped, paired) = (21755852, 1, 21279032, 20217141)
Error rate 0.025004
Uniquely mapping reads (MQ>30) 20375224
PIPELINE 1.4:
153682 raw clusters/tile
131772 post filter clusters/tile
ELAND: 98.14% align, error rate 1.65%
maq-0.7.1 (map -n 3)
[match_data2mapping] 25751286 out of 26342226 raw reads are mapped with
24449419 in pairs.
-- (total, isPE, mapped, paired) = (26342226, 1, 25751286, 24449419)
Error rate 0.021450
Uniquely mapping reads (MQ>30) 24698897
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