User: william.bill.langdon

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Posts by william.bill.langdon

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Answer: A: Gallery: Computational tools for DNA methylation
... [BioData Mining][1] has just published our "Short Report" on Genetically improved BarraCUDA. Bill [1]: http://dx.doi.org/10.1186%2Fs13040-017-0149-1 ...
written 9 weeks ago by william.bill.langdon30
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Answer: A: Gallery: Computational tools for DNA methylation
... New technical report RN/16/10 https://doi.org/10.1101/095075 gives BarraCUDA performance on nvidia Titan X (pascal), GTX 1080 and Titan X (compute level 5.2) graphics cards on paired end Cambridge Epigenetix data. Bill ...
written 10 months ago by william.bill.langdon30
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Answer: A: Gallery: Computational tools for DNA methylation
... The latest version of BarraCUDA (ie 0.7.107f http://sourceforge.net/projects/seqbarracuda/, effectively BWA on CUDA hardware) can be used with epigenetics NGS data on graphics cards. However note that currently epigenetics data effectively doubles the size of the memory needed for the reference geno ...
written 10 months ago by william.bill.langdon30
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Answer: A: Do I have to look for sequence or reverse complement?
... Many of the popular DNA sequence matching tools (eg BWA, BarraCUDA, Bowtie2) include looking for the antisense match by default. Bill ...
written 10 months ago by william.bill.langdon30
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Answer: A: Is there any genome dataset along with its epigenetic related datasets?
... Our paper lists the datasets we used and their locations. See "Benchmarking Genetically Improved BarraCUDA on Epigenetic Methylation NGS datasets and nVidia GPUs" In Genetic Improvement 2016, (GECCO 2016) workshop, pages 1131-1132, 20-24 July, Denver. http://dx.doi.org/doi:10.1145/2908961.2931687 ...
written 10 months ago by william.bill.langdon30
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Answer: A: New Hardware Setup a) Server with Linux b) Server ESX and on top Linux or b) Wor
... BarraCUDA is compatible with BWA indexes but runs on nVidia CUDA GPUs. We just released version 0.7.107f http://sourceforge.net/projects/seqbarracuda/ which has also been used with Epigenetics data Bill http://www.cs.ucl.ac.uk/staff/W.Langdon/ ...
written 10 months ago by william.bill.langdon30
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Comment: C: Comparison Of Soap And Bwa
... Dear Heng, I replied to your email before spotting your posting. So for everyone else here are my thoughts: Yes it does seem that people are moving to longer read lengths. We measured 36bp because that is what the Cancer Institute used. One of the longer term goals of the project is to make it easi ...
written 4.7 years ago by william.bill.langdon30
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Answer: A: Comparison Of Soap And Bwa
... I found Bowtie2GP to be 4 times faster than BWA on some human pair-end alignments, took less than half the memory and almost the same accuracy. See http://arxiv.org/abs/1301.5187 Bill ...
written 4.7 years ago by william.bill.langdon30

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