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How to accelerate genomic sequence alignment 4X using half an FPGA

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re: How to accelerate genomic sequence alignment 4X using half an FPGA
gah4   7/7/2011 8:03:19 AM
Interesting article, but a little behind the current needs. Maybe not so far off for proteins, but for DNA the needs are in the 100TCUPS range. Today, a single DNA sequencer produces 3e9 base/day. To compare against the 3e9 base human genome requires 9e18 CUPD, or about 100TCUPS. First, verilog isn't that hard to use. At the scale needed for DNA, 75% isn't good enough. Note also that the DNA data has been growing faster than Moore's law for many years, with a growth rate of about 1%/week. I have been working on systolic arrays in verilog since the XC4000 days. It is even worthwhile to adjust the datapath widths depending on the need for a given data set, down to about six bits for current sequencers. If you don't like verilog, design a symbolic language for systolic array construction, and a program to translate to verilog. Much easier than trying to coerce C into doing something it wasn't meant to do. -- glen

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