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Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
(Springer Nature, 2008-05-01)
Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of ...
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
(Springer Nature, 2013-04-25)
TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various lengths produced ...
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
(Springer Nature, 2009-03-04)
Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU ...
High-throughput sequence alignment using Graphics Processing Units
(Springer Nature, 2007-12-10)
The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several ...