timkahlke / longread_tutorials Goto Github PK

I was trying to install guppy with this but it says that
wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy_3.4.5_linux64.tar.gz,

but I receive the error:
unable to resolve host address ‘mirror.oxfordnanoportal.com’

Is there any way to install previous versions of guppy?

Ive installed Ubuntu on the VM, but the link to the installation script sends me to a google 404 error - The requested URL was not found on this server.

Is the script no longer available?

sorry, wrong repo

Hi, I have got output fastq files from MinION and merged them into one fastq file. I am looking to get a quality check report and assemble using Unicycler. I tried fastQC for quality check but I think it does not work for MinION data. Also, please let me know how to trim adaptors from the MinION data.

Thank you!

Update to installation script for shasta.

curl -O -L https://github.com/chanzuckerberg/shasta/releases/download/0.6.0/shasta-Linux-0.6.0
chmod ugo+x shasta-Linux-0.6.0
mv shasta-Linux-0.6.0 shasta
......

Shasta also takes fastq now so you can fix this part.

Hello,
I am trying to download the install script and Tutorial data from the Gofile link in LongRead-tutorials, but the website says unable to download data. Is the link still valid?

after running the following command as per your tutorial:
sudo bash ~/Downloads/install_script.sh
and 1 h later (appeared successful installation) i reopened terminal and typed:
guppy_basecaller --print_workflows
i got the message:
" guppy_basecaller: command not found"
any inputs are welcome. All of the above i have run in my stand alone Ubuntu 20.04 laptop

when I run this command
/mnt/c/Users/mdg.bio/Downloads/course_data/practicals/basecalling_practical$ guppy_basecaller –i ./fast5 –s ./guppy_out –c dna_r9.4.1_450bps_hac.cfg --num_callers 2 --cpu_threads_per_caller 1

error: missing required option "save_path"
what I am doing wrong?

Hi Tim,
Thank you SOOOO much for putting this all together this is superuseful and saved my multiple days of my life. Always happy about this.

The code block rendering is sometimes strange as '-' become longer dashes and "'" become "`" or such alike. This generates issues with copy and pasting.... just FYI. I know people should really type it out 👍