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Questions tagged [minion]

Questions associated with the generation or analysis of data from sequencer MinION. For questions about long reads (e.g. including PacBio), use `long-reads` instead. For questions that are more generally about nanopore devices (e.g. including PromethION), use `nanopore` instead.

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Nanopore Flongle vs MinION

How do the Oxford Nanopore Flongle flow cells perform compared to the standard MinION flow cells, when it comes to reliability and error rates? I found this comparison article from last year, from ...
Joel's user avatar
  • 55
1 vote
2 answers
191 views

Help with MinION sequencing data species identification

Hi I'm new to bioinformatics and have just completed my first run on the MinION (long read sequencing Oxford Nanopore Technologies). I was hoping someone could direct me towards R packages, workflow, ...
jack's user avatar
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1 vote
1 answer
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How do I tell that a MinION run has finished based on the files produced?

I want to automate some scripts which should run after a MinION run completes. Is there a file which is produced by MinKNOW which will enable me to tell that the run has finished?
flashton's user avatar
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1 vote
2 answers
453 views

How to demultiplex MinION fastQ files without Porechop?

I recently got fastQ files from a MinION sequencer. I would like to demultiplex these files. Is there any other software to demultiplex (no porechop) in or outside Artic protocol? I would like to ...
Gerald Vasquez Aleman's user avatar
4 votes
0 answers
1k views

Kraken2 > OTU format > Phyloseq

A collaborator has passed me over Kraken2 outputs *.report and *.kraken, from a metatranscriptomic sequencing experiment conducted on the minION. I would like to make a tree if the data using a ...
Reebola95's user avatar
3 votes
2 answers
450 views

Microbial Classification with 16S Nanopore Data

I have recently been tasked with analyzing a heterogeneous microbial sample composed of 16S data generated on a MinION sequencer, with the goal of assigning taxonomies and calculating respective ...
Sparkflyer's user avatar
6 votes
1 answer
4k 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 ...
Mark Amery's user avatar
1 vote
0 answers
3k views

using guppy_basecaller on node with 2 GPUs

I am trying to use the GPU enabled version of the guppy_basecaller on an HPC cluster. I am requesting a node that has 2 GPUs and am requesting 1 of the two GPUs. So, I am trying to set the ...
Bob's user avatar
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6 votes
2 answers
3k views

Demultiplex nanopore reads with custom barcodes

We have a problem trying to demultiplex MinION sequences with custom barcodes. Do you have any software recommendations we can try for demultiplexing or how to demultiplex these custom barcodes with ...
Martín Terán's user avatar
4 votes
1 answer
248 views

Error correction within the long read

I am going to get some data from plasmid sequencing to identify SNPs on the plasmids. What is done in the lab is the following: The plasmids are purified by size. We amplify the plasmids using the ...
Praderas's user avatar
  • 143
1 vote
1 answer
81 views

Using ONT MinION, why is that we cannot get a full length DNA read?

Here, https://www.youtube.com/watch?v=E9-Rm5AoZGw, ONT claims they can read non-fragmented DNA and that with the hairpin like structure the double strands can be read at once. Then why is that MinION ...
Hari Sankar S's user avatar
6 votes
3 answers
1k views

Total reads aligning to each reference within a bam file

I have two PCR amplicons that have been multiplexed and sequenced using the nanopore minion. I have aligned the fastq reads using minimap2 with a reference file containing both amplicon sequences and ...
CM3's user avatar
  • 63
7 votes
1 answer
769 views

Extracting strand specific reads from MinION cDNA-PCR protocol

I recently performed my first MinION run, and now I'm trying to analyze the data. Being pretty new to the bioinformatics field, I was hoping some of you could help me out. As a bit of background, I'...
Amy T's user avatar
  • 71
4 votes
2 answers
4k views

Can I stop my nanopore sequencing run if there are no more reads being produced?

I am sequencing a whole genome on MinION. I have used this flow cell for 6 hours for the phage lambda control. That gave me around 300,000 reads. I started a 48h sequencing run on the same flow cell ...
Biomagician's user avatar
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3 votes
1 answer
1k views

How many reads has my sequencing run produced on minion?

I am running a 48 h sequencing protocol on a FLO-MIN107, on MinION, with DNA library-prepped with SQK-RAD004. MinKNOW is installed on my Mac and controlling the MinION. I have found the following ...
Biomagician's user avatar
  • 2,459
2 votes
1 answer
1k views

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

I download the Albacore wheel from Oxford Nanopore. I activated my conda environment that has Python 3 as the default python version. I tried to install Albacore with ...
Biomagician's user avatar
  • 2,459
2 votes
1 answer
6k views

Set directory where MinKNOW writes FAST5 files

I would like to set the folder in which MinKNOW writes the raw data. How can I do this? I do not currently know where MinKNOW will output my data. What is the default directory where MinKNOW outputs ...
Biomagician's user avatar
  • 2,459
5 votes
2 answers
646 views

Can I use my computer while MinION is sequencing without negatively affecting the run?

I have a Mac Book Pro and I am about to start a sequencing run on the MinION. MinKNOW is going to be running for 2 days. Can I use my computer during sequencing? Can I browse the web and use Excel, ...
Biomagician's user avatar
  • 2,459
2 votes
1 answer
35 views

ENA minion 2D data doesn't actually have 2D data

I am looking at some yeast ONT data from De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms, Giordano et al 2017. I noticed that the Minion fastq files have both a forward and ...
conchoecia's user avatar
  • 3,181
2 votes
1 answer
1k views

What to do with the configuration test cell after configuring the MinION with it?

What to do with the configuration test cell after configuring the MinION with it? I received a MinION with a configuration test cell in it. After running a configuration in the MinKNOW software while ...
Biomagician's user avatar
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11 votes
4 answers
7k 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? ...
Biomagician's user avatar
  • 2,459
3 votes
1 answer
942 views

Does MinKNOW work with Mac OSX high sierra 10.13.1?

I have done a compatibility check as described here on my computer to know if I can use MinKNOW on my mac laptop. It says that my OS is incompatible and that the OSX must be Yosemite or El Capitan. ...
Biomagician's user avatar
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3 votes
2 answers
569 views

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

I run the MinION MinKNOW without the live base-calling option. We know there is Metrichor and Albacore to perform base-calling after this process. However, I have not done any base-calling yet. My ...
andresito's user avatar
  • 385
4 votes
2 answers
523 views

Simulate fast5 MinION run

I'm planning on using Oxford Nanopore MinION sequencer to test a script that I'm working on. However, I would not like to run multiple MinION runs to validate the tool. I'd like to simulate various ...
andresito's user avatar
  • 385
3 votes
2 answers
556 views

Minion channel ID's from Albacore

The latest version of Albacore from Oxford Nanopore Technologies calls bases from raw fast5 files. A useful piece of output is the sequence_summary.txt, which is a ...
roblanf's user avatar
  • 962
2 votes
3 answers
427 views

How do I find the most similar sequences from a large set of short sequences?

I've been asked to evaluate whether the MinION will be sufficient to distinguish between 20bp CRISPR guide RNAs from the GeCKO v2 set. I know that this set has some exactly identical sequences, which ...
gringer's user avatar
  • 14.4k
5 votes
1 answer
217 views

Rapid metagenomics classifiers on long read data [closed]

I recently used the minION (Nanopore, 9.4 flow cell, RAD001 kit) to generate a metagenome out of environmental samples. Passed reads weren't brilliant (196, average 1,594bp lenght), but working with ...
André Soares's user avatar
14 votes
3 answers
2k views

How can I improve the yield of MinION sequencing runs?

This is a frequently-asked question within the nanopore community. Oxford Nanopore currently claims that they are able to generate run yields of 10-15 gigabases (e.g. see here and here), and yet it's ...
gringer's user avatar
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13 votes
2 answers
4k views

Is it possible to perform MinION sequencing offline?

I vaguely remember, that the original plan of Oxford Nanopore was to provide cheap sequencers (MinION), but charge for base-calling. For that reason the base-calling was performed in the cloud, and ...
Iakov Davydov's user avatar