Benjamin Callahan's guest appearances

Benjamin Callahan

the bioinformatics chat

David Kelley

Irineo Cabreros

Romain Lopez

Gabriel Misrachi

Hassan Samee

Kristina Grigaityte

Jacob Schreiber

Simeon Carstens

Trevor Pesout

HoJoon Lee

Seung Woo Cho

Kaushik Panda

Keith Slotkin

Fernando Portela

Chang Xu

OwlTail

In this episode, Benjamin Callahan talks about some of the issues faced bymicrobiologists 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 &amp; 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 &amp; 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!

In this episode, <a href="http://callahanlab.org" rel="nofollow" target="_blank">Benjamin Callahan</a> talks about some of the issues faced by microbiologists when conducting amplicon sequencing and metagenomic studies. The two main themes are: <ul> <li>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.</li> <li>Why abundances inferred from community sequencing data are biased, and how we can model and correct this bias.</li> </ul> Links: <ul> <li><a href="http://dx.doi.org/10.1038/ismej.2017.119" rel="nofollow" target="_blank">Exact sequence variants should replace operational taxonomic units in marker-gene data analysis</a> (Benjamin J Callahan, Paul J McMurdie &amp; Susan P Holmes)</li> <li><a href="http://dx.doi.org/10.1038/nmeth.3869" rel="nofollow" target="_blank">DADA2: High-resolution sample inference from Illumina amplicon data</a> (Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson &amp; Susan P Holmes)</li> <li><a href="https://doi.org/10.1128/mBio.02149-17" rel="nofollow" target="_blank">In Nature, There Is Only Diversity</a> (Michael R. McLaren, Benjamin J. Callahan)</li> <li><a href="https://doi.org/10.7554/eLife.46923.001" rel="nofollow" target="_blank">Consistent and correctable bias in metagenomic sequencing experiments</a> (Michael R McLaren, Amy D Willis, Benjamin J Callahan)</li> </ul> If you enjoyed this episode, please consider supporting the podcast on <a href="https://www.patreon.com/bioinfochat" rel="nofollow" target="_blank">Patreon</a>!

#39 Amplicon sequence variants and bias with Benjamin Callahan