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More complete assemblies were obtained using Illumina sequencing [ 28].
These longer reads in turn resulted in more complete assemblies.
2. For the perfect assemblies, increasing sequencing depth and average read length will result in more complete assemblies.
When k is small, the larger number of splicing graphs resulted in more complete assemblies, although the sequences were shorter and thus more fragmented.
For comparison, Illumina data were sampled at the same seven depths of coverage as the PacBio data and assemblies were performed, however, none returned more complete assemblies than that performed with 9111× depth of coverage.
While a higher number of missassemblies may occur in smaller k-mer length assemblies, it is believed that assemblies with varying k-mer lengths will produce more complete assemblies [ 38].
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To be clear, reads of 1000nt in length, or a mate pair separated by the same distance, will produce a more complete assembly than unpaired 75nt reads.
The goal is to then independently extend each contig to produce a more complete assembly.
Many of these intervening gaps can subsequently be filled using PBJelly software, ultimately resulting in a more complete assembly [ 19].
This information will be valuable to search for additional TAAR genes when a more complete assembly of the Atlantic salmon genome becomes available (S. Lien et al. in preparation).
Three types of sequencing run were performed in an effort to obtain sequence data that would enable more complete assembly of genomic regions containing repetitive sequences; these consisted of a 454 single reads, 454 paired reads with an insert size of 2.5 kb, and Illumina paired reads with an insert size of 3.5 4 kb.
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more contiguous assemblies
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more complete ones
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more complicated assemblies
more continuous assemblies
more complete opportunities
more robust assemblies
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