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This Week in Genome Research: Apr 26, 2017

University of Rochester researchers report on findings from a study that set out to profile repetitive satellite DNA in the fruit fly Drosophila melanogaster using long reads produced by Pacific Biosciences single-molecule sequencing. The team applied this strategy to sequencing complex satellite DNA loci on Drosophila's autosomal chromosome before comparing related assembly and analysis pipelines. From their initial fruit fly findings, for example, the study's authors saw signs of "higher-order structure within [satellite DNA] arrays," consistent with recent structural rearrangements."

David Jaffe and colleagues from 10x Genomics outline a de novo assembly method for putting together diploid human genome sequences. The team partitioned the genome with a 10x Genomics microfluidics platform before subjecting the sample to Illumina HiSeq X sequencing and assembling the reads with an algorithm called Supernova. Using this approach, it successfully sequenced seven human samples, producing assemblies with contigs that exceeded 100,000 bases and phased blocks of sequence stretching out beyond 2.5 million bases. The authors note that "the laboratory and computational methods are encapsulated in a complete commercial system from 10x Genomics."

Finally, investigators from Hanyang University in Korea introduce a pipeline dubbed CAFE that's designed to assemble transcriptome maps that include RNA sequencing data for both stranded and unstranded transcript reads (those without an established orientation) using a computational step designed to help orient the latter reads. The team demonstrated that it could predict the orientation of hundreds of billions of unstranded reads using RNA sequence data from efforts such as ENCODE, the Cancer Genome Atlas, GTEx, and Human BodyMap 2.0 in the analysis, subsequently putting together transcriptome maps that contained new and known long non-coding RNAs.