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Tampa area television stations reported that a neighboring pool appears to have cracks.
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Nucleotide accuracy was assessed by comparing the overlaps between neighboring pools.
These reads from both neighboring pools were combined and reassembled with Newbler.
(3) Contigs in overlap regions between neighboring pools were identified from both pools via alignments with MUMMER version 3.20 (Delcher et al. 2002).
Since regions between neighboring pools overlapped, we implemented a third step to the assembly protocol in order to make these regions nonredundant and to improve their quality.
This third step entailed comparing the assemblies from neighboring pools and identifying the contigs and underlying reads in the overlapping regions.
Secondly, we assessed nucleotide accuracy by comparing those regions of O. barthii that lay in the overlapping regions between neighboring pools and were therefore sequenced twice.
For each pair of neighboring pools, contigs from the initial Newbler assembler (prior to combining overlaps) were aligned to each other using BLASTN (Altschul et al. 1990).
Assembly accuracy of the initial 454 Newbler assembly (stage 1) was assessed by comparing the overlap regions of neighboring pools using BLASTN (Altschul et al. 1990).
SMDA generates all possible combinations of label assignments to those neighboring pools and reactions.
The protocol uses * key pools such that neighboring key pools have more keys in common.
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