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#39 Amplicon sequence variants and bias with Benjamin Callahan
MP3•Episode home
Manage episode 247198683 series 1537951
Content provided by Roman Cheplyaka. All podcast content including episodes, graphics, and podcast descriptions are uploaded and provided directly by Roman Cheplyaka or their podcast platform partner. If you believe someone is using your copyrighted work without your permission, you can follow the process outlined here https://player.fm/legal.
In this episode, Benjamin Callahan talks about some of the issues faced by microbiologists when conducting amplicon sequencing and metagenomic studies. The two main themes are:
- Why one should probably avoid using OTUs (operational taxonomic units) and use exact sequence variants (also called amplicon sequence variants, or ASVs), and how DADA2 manages to deduce the exact sequences present in the sample.
- Why abundances inferred from community sequencing data are biased, and how we can model and correct this bias.
Links:
- Exact sequence variants should replace operational taxonomic units in marker-gene data analysis (Benjamin J Callahan, Paul J McMurdie & Susan P Holmes)
- DADA2: High-resolution sample inference from Illumina amplicon data (Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson & Susan P Holmes)
- In Nature, There Is Only Diversity (Michael R. McLaren, Benjamin J. Callahan)
- Consistent and correctable bias in metagenomic sequencing experiments (Michael R McLaren, Amy D Willis, Benjamin J Callahan)
If you enjoyed this episode, please consider supporting the podcast on Patreon.
70 episodes
MP3•Episode home
Manage episode 247198683 series 1537951
Content provided by Roman Cheplyaka. All podcast content including episodes, graphics, and podcast descriptions are uploaded and provided directly by Roman Cheplyaka or their podcast platform partner. If you believe someone is using your copyrighted work without your permission, you can follow the process outlined here https://player.fm/legal.
In this episode, Benjamin Callahan talks about some of the issues faced by microbiologists when conducting amplicon sequencing and metagenomic studies. The two main themes are:
- Why one should probably avoid using OTUs (operational taxonomic units) and use exact sequence variants (also called amplicon sequence variants, or ASVs), and how DADA2 manages to deduce the exact sequences present in the sample.
- Why abundances inferred from community sequencing data are biased, and how we can model and correct this bias.
Links:
- Exact sequence variants should replace operational taxonomic units in marker-gene data analysis (Benjamin J Callahan, Paul J McMurdie & Susan P Holmes)
- DADA2: High-resolution sample inference from Illumina amplicon data (Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson & Susan P Holmes)
- In Nature, There Is Only Diversity (Michael R. McLaren, Benjamin J. Callahan)
- Consistent and correctable bias in metagenomic sequencing experiments (Michael R McLaren, Amy D Willis, Benjamin J Callahan)
If you enjoyed this episode, please consider supporting the podcast on Patreon.
70 episodes
All episodes
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