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Questions tagged [base-calling]

The process of transforming the raw signal of a sequencer (light, images, electrical signal) into DNA or RNA bases. For Illumina, the basecalling consists of transforming the pictures with lights of different colours into bases. For Nanopore, it consists in transforming the electrical signal into bases. Basecalling can also include the calculation of the probability of the called base being correct (PHRED score). Albacore is a basecaller for Nanopore data.

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1answer
196 views

How does MinKNOW classify 1D reads as “pass” or “fail”?

I have found a couple of sources1,2 that indicate that a read in a 1D² run is classified by MinKNOW as "pass" and put into the fastq_pass folder if both of the ...
6
votes
1answer
291 views

Albacore basecalling running but outputs 0 reads

I am trying to basecall data produced by the MinION using the SQK-LSK109 kit and FLO-MIN106 flowcell via the command-line. My version of albacore is the latest (v2.3.4). I tried running using the ...
7
votes
4answers
4k views

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

What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing? I am about to start a MinION run on my laptop. What should I consider when choosing my basecaller? ...