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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3 votes
1 answer

Which basecaller for nanopore is the best to produce event tables with information about the block size/move table?

I previously used albacore version 2.3.1 to make initial move tables, but then I re-squiggle using Tombo version 1.5.1 to fix the errors. Example of move table produced by albacore, in which all the ...
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1 vote
1 answer

Reading a Fast5-file with Python

I am trying to extract data from fast5-file with python 3.9.13 in Ubuntu. I have found a library "fast5_research"(This package comprises an API to HDF containers used by the research groups ...
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1 vote
1 answer

Extracting base sequences from ABI/AB1 sanger sequencing chromatogram

I am trying to understand the sanger sequencing ABI/AB1 file format better, and extract base calls from given signal intensities over time. As I understand, reading in a raw AB1/ABI file into python, ...
  • 11
1 vote
1 answer

Upgrading guppy basecaller on Oxford Nanopore Gridion via PPA

I am trying to update the guppy_basecaller (current version installed is 3.2.10+aabd4ec) on a ONT Gridion device. I am initially trying to update it via the ...
  • 273
0 votes
1 answer

nanopore - where to retrieve information from the basecaller used

Where can I find information about the basecaller used in a specific nanopore run (we have a Gridion machine)? I know already that we have Guppy v. 3.0.3, which I ...
  • 273
6 votes
1 answer

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
1 answer

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 ...
  • 621
11 votes
4 answers

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? ...
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