7 votes

What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing?

There are also third party free and open source basecallers that haven't been developed by Oxford Nanopore. Of particular note is Chiron, which gave the best uncorrected assembly identity among the ...
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5 votes
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What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing?

First of all - yes, you can generate FAST5 files and basecall later. Basecalling during the sequencing run is useful if you want results more quickly. You can also recall your FAST5 files with ...
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5 votes
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Albacore basecalling running but outputs 0 reads

I believe you have multiread fast5 files, as generated by recent versions of MinKNOW. A conversion script is available to convert these to the older, one-read one-file format. AFAIK Albacore is being ...
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5 votes

What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing?

It's worth noting two things as of Dec 2018: Albacore is being deprecated (but is still available from the Nanopore developer portal). Guppy is under active development, so Ryan Wick's comparisons ...
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4 votes
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How does MinKNOW classify 1D reads as "pass" or "fail"?

The classification is indeed based purely on comparing a mean to a threshold... but it's not the mean of the Phred scores that represent base quality on a logarithmic scale, but rather the mean of the ...
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2 votes

nanopore - where to retrieve information from the basecaller used

I basecall separately with guppy. In the output folder specified by --save_path or -s there are a whole bunch of .log files. <...
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1 vote

Upgrading guppy basecaller on Oxford Nanopore Gridion via PPA

This is an ONT problem, not an ubuntu problem. Keys can expire over time, and need to be updated. The keys for the Guppy basecaller are not present in the ubuntu repository; you need to get them from ...
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1 vote

What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing?

Depending on your local system I'd suggest to run the MinION without local basecalling, and perform basecalling later using Albacore on server/cluster. That will keep storage requirements on your ...
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