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Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result
3mo
ok, that figure looked fine in the preview but was transparent, here's a better version
3mo
Pรกll Melsted
Pรกll Melsted
For a large dataset (295M reads) the GPU version took 50 seconds. Just running zcat on the files takes 10 minutes! Decompression and parsing FASTQ is a major bottleneck . Instead of using kseq we moved this work parsing to the GPU which delivers amazing throughput.
๐—ฃ๐—ผ๐˜€๐˜๐—ฑ๐—ผ๐—ฐ ๐—ฎ๐—ป๐—ฑ ๐—ฃ๐—ต๐—— ๐—ฝ๐—ผ๐˜€๐—ถ๐˜๐—ถ๐—ผ๐—ป๐˜€ ๐—ถ๐—ป ๐—–๐—ผ๐—บ๐—ฝ๐˜‚๐˜๐—ฎ๐˜๐—ถ๐—ผ๐—ป๐—ฎ๐—น ๐—š๐—ฒ๐—ป๐—ผ๐—บ๐—ถ๐—ฐ๐˜€ / ๐—”๐—น๐—ด๐—ผ๐—ฟ๐—ถ๐˜๐—ต๐—บ๐—ถ๐—ฐ ๐—•๐—ถ๐—ผ๐—ถ๐—ป๐—ณ๐—ผ๐—ฟ๐—บ๐—ฎ๐˜๐—ถ๐—ฐ๐˜€ I am currently recruiting for both: ๐Ÿ”น Postdoc position su.varbi.com/what:job/job... ๐Ÿ”น PhD position su.varbi.com/en/what:job/... Please share with anyone who might be interested!