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Genomic contigs were generated and assembled by using the Newbler assembler software (Roche Diagnostics, Basel, Switzerland).
Genomic contigs were generated and assembled by using the Newbler assembler software (Additional file 2: Table S3).
To evaluate the improvement in assembly quality with mate-pairs information we generated and assembled datasets similar to simHC, simLC and simMC with paired-ended reads of insert length 2000 bases.
This diversity poses general questions for neural circuit analysis: how are these interneuron cell types generated and assembled into stereotyped local circuits and how do they differentially contribute to circuit operations that underlie cortical functions ranging from perception to cognition?
Briefly, from the previous study, 438,321 ESTs were generated and assembled into contigs and singletons [11].
Six Gbp of data were generated and assembled into unigenes.
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The development of a draft genome sequence using SGS technologies generally involves three main steps: generating and assembling short sequence reads into longer DNA contigs, ordering contigs along chromosomes, and annotating protein-coding genes and other elements for the contigs [ 1, 2].
PHRED and PHRAP [ 43, 44] were used to generate and assemble raw data.
Therefore, new methods are required to generate and assemble large datasets, many of which currently consist of substantially shorter reads.
In the absence of an affordable and capable technology to generate and assemble a conifer genome, previous investigations have relied on other techniques to generate sequence for basic and applied research in pine genetics.
Our capability to generate and assemble a draft sequence for an entire mammalian genome indicates that such technology can be used to generate many other mammalian genome draft sequences in a time- and cost-effective manner.
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