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The gsMapper software utilizes a reference sequence to aid the assembly of raw read data.
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While sequencing the first tier with 454-FLX system alone was inefficient for SNP discovery in common bean, it did produce 300 to 350 bp sequences which we were able to utilize as a reference sequence to align the shorter, but much more numerous, GA sequences.
RNA-Seq obtains gene expression estimates by assigning next-generation sequencing (NGS) reads to transcripts, either by mapping to a reference sequence, or assembling into contiguous stretches of sequence data (contigs) utilizing overlapping sequence amongst the reads themselves.
The sequence reads obtained were subjected to multiple alignments together with a reference sequence for the corresponding genomic locus.
One is used as a reference sequence, and the other is shifted relative to the reference.
braziliensis M2904 genome as a reference sequence.
Comparative assembly [ 31] utilizes a reference genome sequence as a guide to discern repeat contigs.
The search skills game or a reference sequencing game.
In addition, an approach that utilizes multiple reference sequences representing known variation in the region could potentially be useful in some instances, both to capture all sequence reads for the region and to avoid reference bias.
Further, the arrays were developed utilizing the BTx623 reference sequence and do not capture polymorphisms, copy number variation and presence-absence variation across all the sampled genotypes.
On finalization of an allotetraploid cotton physical map, BES-associated SNPs can also be utilized to integrate unplaced contigs and singletons to enhance the completion of a quality draft reference sequence.
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