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Mixed clone reads containing vector sequence was the second most prevalent process-related failure mode.
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We construct three types of read sets that consist of all reads that putatively overlap a region of the genome delineated by clone extent endpoints: For each clone we create a clone read set, which contains all the reads overlapping the clone (including reads from other clones) (Figure 6a).
Given a read set, we determine if its contigs belong to Bi, as follows: Clone read sets.
The second most prevalent failure mode in the "process related" category, "Mixed clone with vector sequence" (30% of reads in this classification), is likely a result of two side by side colonies being picked into the same well or through contamination originating from the use of automated liquid handlers.
The peak densities of asexual parasites did not differ between Thai and SL clone infections (χ1 = 0.3 P = 0.629), but were both significantly higher than those in mixed clone infections (combined single clones vs. mixed clone χ1 = 6.3 P = 0.012).
This effect of co-infection was confirmed with a comparison of the mixed clone with the 2 single clone type infections grouped together (parasite density χ1 = 14.2, P < 0.001; combined single clones vs. mixed clone: χ1 = 5.8, P = 0.016).
Thus, we additionally examine the relationship between anaemia and transmission in single and mixed clone infections.
Despite the presence of mixed clones within one well, traces often yielded discernable sequence with read lengths broadly distributed up to the Q20: 500–599 bp bin.
The assembly of multiple genomes from mixed sequence reads is a bottleneck in metagenomic analysis.
First, MetaVelvet decomposes a de Bruijn graph constructed from mixed short reads into individual sub-graphs.
Mixed clones were screened and cultured for an additional 4 weeks.
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