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Fig. 2 | BioData Mining

Fig. 2

From: Genetically improved BarraCUDA

Fig. 2

Processing paired end DNA sequences. “aln” is run two times (once per end), potentially in parallel, and its alignments are piped or passed via intermediate.sai files (dashed blue arrows) into “sampe” (sam (pe) paired end). “sampe” may be run in parallel. It also reads the index of the reference human genome and both ends of each DNA sequence in order to give the combined alignment in sam format. In the case of BarraCUDA, the two “aln” process each use a GPU and “sampe” uses multiple host threads. For bwa “aln” uses multiple host threads but “sampe” is single threaded

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