We are using Miseq to sequence microbial genomes (~5Mb). In the first run (1#), library containing 12 samples were sequenced, and 6 samples were sequenced in the other run (2#). Obviously, the data of the 2# run have higher coverage depth that those of the 1# run. Therefore, I expected that the quality of de novo assembly data of the 2# run should be better than those of the 1#run. After analyzing by CLC Bio, I found that it is not true. Each sample from these two runs are shown as follow:
Sample of 1# run Sample of 2# run
N50 192439 261691
Max length 461804 450288
Average length 38501 8334
Count of contig 145 688
I dont understand why there are more contigs of 2# run that 1# run? Is that because of the high coverage? And how about the de novo assembly of these two runs?
Thank you very much!
Sample of 1# run Sample of 2# run
N50 192439 261691
Max length 461804 450288
Average length 38501 8334
Count of contig 145 688
I dont understand why there are more contigs of 2# run that 1# run? Is that because of the high coverage? And how about the de novo assembly of these two runs?
Thank you very much!
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