Getting the most out of Machines

Chapters:

00:00 PhiX

14:30 low complexity

19:30 UMIs

32:10 FastQC

43:00 MultiQC

56:40 PycoQC

PhiX concentrations for loading a validation run:https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000001536

Dnatech on why UMIs are used:https://dnatech.genomecenter.ucdavis.edu/faqs/what-are-umis-and-why-are-they-used-in-high-throughput-sequencing/

BMH learning on UMIs: https://www.youtube.com/watch?v=sRPMsnhIBK0

FastQC for QC of .fastq(.gz) files:https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

A FastQC report from a „good“ sample:https://www.bioinformatics.babraham.ac.uk/projects/fastqc/good_sequence_short_fastqc.html

multiqc for summarizing QC reports: https://multiqc.info/

UMI-tools for working with UMI data: https://umi-tools.readthedocs.io/en/latest/

pycoQC for Nanopore QC: https://github.com/a-slide/pycoQC

Since 2018, West German Genome Center (https://wggc.de/)operates as the next generation sequencing facility and supportsresearch in genomics & transcriptomics by providing expertise andsequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/)- network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ).

The Explain Podcast is recorded at the Medienlabor atHeinrich-Heine University of Düsseldorf (https://medienlab.phil.hhu.de/). Our podcast is an outreach activity within the national genomics facility "West German Genome Center" funded by the DFG (https://www.dfg.de/) (No. 407493903).

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠