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 |
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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.
NOTE: 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/
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Once logged in you will be able to access the conda “base” environment
Configure conda channels https://bioconda.github.io/
| Code Block |
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conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict |
Source for information below: https://astrobiomike.github.io/unix/conda-intro
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