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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

...

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

NOTE: if you have already installed conda then you do not need to do the steps below

Download Miniconda installer for your system https://docs.anaconda.com/free/miniconda/

...