Overview of today’s session:
Learn to use CONDA to install tools and create conda environments
Hands-on exercises:
Quality Control (QC) of raw Nanopore data
Mapping of processed Nanopore data onto a reference genome
Run the epi2me-labs/wf-human-variation nextflow pipeline
Public Nanopore Datasets
Experiment Accession | sample | FASTQ | Experiment Title | Organism Name | Instrument | Submitter | Study Accession | Study Title | Sample Accession | Total Size, Mb | Total Spots | Total Bases | Library Strategy | Library Source | Library Selection |
SRX14748451 | S1 | SRR18645307 | Homo sapiens | Homo sapiens | MinION | Drexel University | SRP367676 | Multiplex structural variant detection by whole-genome mapping and nanopore sequencing. | SRS12509856 | 821.1 | 348226 | 972620520 | OTHER | GENOMIC | other |
ERX8211413 | S3 | ERR8578833 | MinION sequencing | Homo sapiens | MinION | the university of hong kong | ERP135493 | Target enrichment sequencing and variant calling on medical exome using ONT MinION | ERS10590135 | 8961.02 | 9636172 | 10382057986 | Targeted-Capture | GENOMIC | PCR |
SRX13322984 | S5 | SRR17138639 | Nanopore targeted sequencing (ReadUntil/ReadFish) of NA12878-HG001- basecalled sequences | Homo sapiens | MinION | Garvan Institute of Medical Research | SRP349335 | Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing | SRS11230712 | 6629.97 | 5513156 | 7815960904 | WGS | GENOMIC | other |
SRX13323057 | S6 | SRR17138566 | Nanopore targeted sequencing (ReadUntil/ReadFish) of NA12878-HG001- basecalled sequences | Homo sapiens | MinION | Garvan Institute of Medical Research | SRP349335 | Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing | SRS11230747 | 17107.98 | 12278391 | 20238395479 | WGS | GENOMIC | other |
What is conda?
Conda is a powerful command line tool for package and environment management that runs on Windows, macOS, and Linux.
Installing conda
Source: https://conda.io/projects/conda/en/latest/user-guide/install/index.html
To install conda, you must first pick the right installer for you. The following are the most popular installers currently available:
Miniconda
Miniconda is a minimal installer provided by Anaconda. Use this installer if you want to install most packages yourself.
Anaconda Distribution
Anaconda Distribution is a full featured installer that comes with a suite of packages for data science, as well as Anaconda Navigator, a GUI application for working with conda environments.
If you have already installed conda then you do not need to do the steps below |
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Download Miniconda installer for your system https://docs.anaconda.com/free/miniconda/
As we are working with the HPC (Linux) copy and paste the following to your terminal to install Miniconda:
mkdir -p ~/miniconda3 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3 rm -rf ~/miniconda3/miniconda.sh
After installing initialise the newly installed Miniconda by running the following:
~/miniconda3/bin/conda init bash