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Finally, the intrascaffold gaps were filled using the paired-end extracted reads.
The extracted reads were de novo assembled to compile the genomic sequences flanking the inserted plasmid.
The extracted reads were further clustered into nonredundant reads using USEARCH/UCLUST program v5.1 [ 67].
The extracted reads were assembled with Trinity using the parameters described above.
The extracted reads were taxonomically classified using the SILVAngs server (33).
We extracted reads containing ≥30 consecutive adenine nucleotides at their 3'end.
Similar(33)
These extracted read pairs were then mapped to the Greengenes database using BWA-MEM v0.7.5a-r405 (Li and Durbin 2010).
In order to reconstruct breakpoint junctions, we sequenced FRAG00062 to 100× coverage, extracted read pairs from the ends of duplicated and triplicated blocks and performed de novo assembly.
One diary extract reads: "Alex was interesting on the Howard stuff.
Each day NELL extracts (reads) more facts from the web, and integrates these into its growing knowledge base of beliefs.
The extract reads: "Britain is proud of its tradition of providing a safe haven for people fleeting (sic) persecution and conflict".
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com