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Basecalling of Nanopore Raw file

Hello, I am working on Oxford Nanopore Technologies device MinION with MinKNOW software for De Novo Whole Genome Sequencing. After sequencing basecalling with guppy tooks longer time. Considering time as factor only species identification from 20% basecalled data is enough or wait for complete basecall.

sequencing next-gen genome
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written by AS-git • AS-git

To speed up the process you can use guppy with the fast mode option. Perhaps it will still be accurate enough for species identification

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written by samuel.a.odonnell samuel.a.odonnell

1 answer

To perform basecalling of Minion data in a reasonable time, you have to use a GPU with CUDA. Our laboratory uses Nvidia GeForce 2080Ti, and basecalling usually takes about 10 hours. On a CPU with 40 threads it takes about a week.

Whether 20% of reads are enough for species identification depends highly on what you sequenced. If it's a complex metagenome, then I recommend to wait until basecalling finishes.

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written by shelkmike shelkmike

Thanks a lot for your suggestion, I have a doubt that in between 20% and 100% basecall, Is it like a base in a particular position for 20 times and 100 times respectively or 20% basecall shows 20% of whole genome and 100% shows total genome size.

Thank you

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written by AS-git • AS-git

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