Dear all,
I tried to compare the P6C4 and P5C3 chemistries.
P6C4 E coli K12 raw data from:
P5C3 E coli K12 raw data from: (referred by the PBcR site)
P6C4 P5C3
Total 780M 374M
Coverage 168x 80x
avgReadLen 11074 8682
stdevReadLen 7107 5394
longestRead 41390 28647
I ran them through the PBcR-quiver pipeline and then use QUAST to evaluate the results:
PBcR-quiver(P6C4) PBcR-quiver(P5C3)
#misassemblies 5 3
#local_misassemblies 2 2
duplication_ratio 1.003 1.0
bases_not_covered 93 5756 (reference has 4641652bp)
#mismatches 4 2
#indels 27 3 (indels is the number of indels not number of indels in basepairs)
#genes 4513+3p 4508+2p (total 4516 genes, p means partial)
We can see that the coverage is a lot better most likely due to longer read length and higher throughput. But the errors also increased significantly even though the throughput doubled. What do you think was the cause? Different labs perhaps? What's your experience with the two chemistries?
I tried to compare the P6C4 and P5C3 chemistries.
P6C4 E coli K12 raw data from:
P5C3 E coli K12 raw data from: (referred by the PBcR site)
P6C4 P5C3
Total 780M 374M
Coverage 168x 80x
avgReadLen 11074 8682
stdevReadLen 7107 5394
longestRead 41390 28647
I ran them through the PBcR-quiver pipeline and then use QUAST to evaluate the results:
PBcR-quiver(P6C4) PBcR-quiver(P5C3)
#misassemblies 5 3
#local_misassemblies 2 2
duplication_ratio 1.003 1.0
bases_not_covered 93 5756 (reference has 4641652bp)
#mismatches 4 2
#indels 27 3 (indels is the number of indels not number of indels in basepairs)
#genes 4513+3p 4508+2p (total 4516 genes, p means partial)
We can see that the coverage is a lot better most likely due to longer read length and higher throughput. But the errors also increased significantly even though the throughput doubled. What do you think was the cause? Different labs perhaps? What's your experience with the two chemistries?
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