Has anyone conducted a duplex analysis on nanopore sequencing data using dorado or any other tools, such as Guppy, Nanopolish, or Medaka?

Aspasia Dimitriadou @Aspasia-Dimitriadou

05 December 2023 1 4K Report

I would appreciate having a discussion with someone who has experience conducting duplex analysis with one of these tools, as I am encountering difficulties with dorado, likely due to the specifications of my computer.

Hai-Trieu Phong

I have tried dorado duplex, but I conducted basecalling on Linux. I obtained the output of MinKnow (recent version) so I think it would be better if I used dorado (duplex) instead of guppy :D

Badges
Science topic

Similar topics
Physical Sciences
Energy

More Aspasia Dimitriadou's questions See All

What is an acceptable small sample size to carry out principal component analysis for a rating scale with 16 items???

Hi Can someone tell me what would be an acceptable sample size for principal component analysis for a rating scale with 16 items. Thanks!

30 March 2020 9,756 3 View

How to insert image in introductory text of survey in Opinio?

Hi I need some technical help. I am trying to insert an image in the introduction of a survey in Opinio. I click on 'insert image' button, then I am prompted to paste the url of the desired image,...

28 March 2020 1,543 3 View

Alternatives to .45 um filter to isolate MS2 from lysed E. coli?

Hello, I am looking for alternatives or cheaper materials to isolate out MS2 from E. coli following lysis via chloroform. Some literature I have reviewed uses a .45 um nanopore filter following...

02 February 2021 807 3 View

Does anyone have experience using High Molecular Weight DNA Extraction Kits for extracting DNA from plant leaves?

Hi there, I'm looking for a High Molecular Plant DNA Extraction Kit for subsequent Nanopore sequencing. Does anyone have experience using commercially available kits? Any...

03 January 2021 9,487 4 View

A light for the oxford nanopore rapid attachment chemistry. Does anyone know how this works?

Some Oxford Nanopore kits have Primers with 5 ' modification that provide ligation to adapters without the need for ligases (ligase-free method), as in 16S barcoding kits. Does anyone know what...

21 December 2020 8,612 3 View

Can Oxford Nanopore Sequencing reads from PromethION sequencer be mapped using the same software as MinION reads? If not please suggest a platform?

I awaiting whole-genome sequencing reads from the ONT PromethION sequencer. I want to know which sequence mapping tool can I use for those reads? The genome is S.cereviseae and I don't know if a...

22 November 2020 944 3 View

How to prepare a solvated Nano-porous graphene sheet system for LAMMPS using VMD?

Hi, I am going to perform MD simulation for the Nanoporous Graphen sheet. I know how to make the pores in VMD. But when I tried to make the data file it was lacking a lot of parameters such as...

20 November 2020 3,629 2 View

What the best way to improve Illumina genomic assembly with nanopore metagenomic data?

I have the Illumina reads and assembly of my bacteria from pure culture DNA sequencing and the nanopore sequencing data from the metagenome (DNA of co-culture). Does anyone know the best way to...

14 July 2020 6,516 3 View

Does metal vapor diffuse/infiltrate into porous thin films during PVD?

Hello everyone, I am depositing 100 nm Ti on porous thin films (200 nm thickness, pore size 3-30 nm) using E beam physical vapor deposition. The coating looks good but I am not sure if Ti vapor...

23 February 2020 5,726 3 View

Does metal vapor diffuse/infiltrate into porous thin films during PVD?

Hello everyone, I am depositing 100 nm Ti on porous thin films (200 nm thickness, pore size 3-30 nm) using E beam physical vapor deposition. The coating looks good but I am not sure if Ti vapor...

01 February 2020 960 3 View

What electrochemical reactions happen in a nanopore experiment using Ag/AgCl electrodes in NaCl solution?

I am using the resistive pulse technique to measure the size of nanoparticles. To do so, a nanopore of known size and shape is placed in an electrolytic solution (PBS, which is mostly NaCl). An...

01 February 2020 6,183 3 View

What is the best protocol for extracting DNA from Gram Negative bacteria for NGS by Nanopore technology?

I need to sequence the genome of Gram negative bacteria by Nanopore technology.

09 October 2019 5,962 6 View