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We will be able to better assess assembly accuracy and design non-redundant probes for every unique gene when the Lumbricus genome is released [36], [41], [42].
We did not reassemble Sanger and 454 sequences because of the lack of an independent and reliable measure to assess assembly quality and accuracy.
Therefore an additional level of verification was necessary to better assess assembly accuracy.
To further assess assembly accuracy, population recombination rates between adjacent SNPs were assessed.
We used CEGMA [ 45] to assess assembly completeness and QUAST 3.0 [ 46] to assess genome assembly metrics.
This model produces highly recombinant data on average, posing challenges for assembly and can be used to assess assembly quality.
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We assessed assembly of these data using three de Bruijn k-mer-based assemblers, chosen either for their widespread use (CLC), or for their claimed performance in a metagenomic setting (CAMERA, IDBA_UD).
Based on these results, the investigative process proves useful in assessing assembly system complexity relative to a working design (complexity ratio) and mean cycle time.
Important to consider HCV transmission route when assessing assembly inhibitors.
We also assessed assembly integrity and completeness by comparison to four reference datasets.
We show that NGS assemblies suffer from indels and substitution errors that are somewhat masked by common metrics for assessing assembly quality.
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