5 votes
Accepted

Demultiplex nanopore reads with custom barcodes

I've written some Perl code for demultiplexing nanopore reads using LAST. A workflow demonstrating the use of this script (and how it works under the hood) can be found here: https://dx.doi.org/10....
gringer's user avatar
  • 13.9k
5 votes
Accepted

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 ...
Wouter De Coster's user avatar
4 votes
Accepted

Can we use non base-called fast5 files in poretools?

No, poretools does not do basecalling. The poretools fastq command can be used to extract the FASTQ information from the basecalled FAST5 file (via MinKNOW live-...
Scot's user avatar
  • 782
3 votes
Accepted

Minion channel ID's from Albacore

There are actually 2048 usable sequencing wells, hexagonally packed with four wells connected to the same sequencing sensor/channel via a multiplex (mux) selector. The combination of the mux and the ...
gringer's user avatar
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3 votes
Accepted

Basecalling process carried out by full_1dsq_basecaller.py/.exe

My understanding is that the 1D$^2$ process is carried out in three stages: Carry out a 1D calling of reads (i.e. what the standard Albacore does at the moment) Link reads that are similar to each ...
gringer's user avatar
  • 13.9k
3 votes

Demultiplex nanopore reads with custom barcodes

There are two other ways in which you could demultiplex reads if guppy doesn't have the config file for the kit you are using. Minibar: This works for dual index barcodes specifically Porechop: This ...
Mrinalini Erkenswick Watsa's user avatar
2 votes

Albacore wheel not supported on this platform (Mac OS X El Capitan)

Not sure about conda as I don't use it, but I can highly recommend pipenv which is the python.org recommended package management ...
Michael Hall's user avatar
1 vote

Can we use non base-called fast5 files in poretools?

Albacore can be used to create a fastq, directly from your fast5 files. As such there is no more reason to use poretools, expect perhaps for getting some metadata. With regards to metadata I would ...
Wouter De Coster's user avatar
1 vote

Minion channel ID's from Albacore

poRe has a show.layout() function which shows you the 32*16 grid on which the channels are arranged. EDIT: THIS APPEARS NOT TO BE THE CORRECT PHYSICAL LAYOUT. <...
Wouter De Coster's user avatar

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