The bioinformatics chat is a podcast about computational biology, bioinformatics, and next generation sequencing.
The bioinformatics chat is produced by Roman Cheplyaka.
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HiFi reads and HiCanu with Sergey Nurk and Sergey Koren (#46)
May 27, 2020
In this episode, I continue to talk (but mostly listen) to Sergey Koren and Sergey Nurk. If you missed the previous episode, you should probably start there. Otherwise, join us to learn about HiFi reads, the tradeoff between read length and quality, and what tricks HiCanu employs to resolve highly similar repeats.
Genome assembly and Canu with Sergey Koren and Sergey Nurk (#45)
May 20, 2020
In this episode Sergey Nurk and Sergey Koren from the NIH share their thoughts on genome assembly. The two Sergeys tell the stories behind their amazing careers as well as behind some of the best known genome assemblers: Celera assembler, Canu, and SPAdes.
DNA tagging and Porcupine with Kathryn Doroschak (#44)
April 29, 2020
Porcupine is a molecular tagging system—a way to tag physical objects with pieces of DNA called molecular bits, or molbits for short. These DNA tags then can be rapidly sequenced on an Oxford Nanopore MinION device without any need for library preparation.
In this episode Katie Doroschak explains how Porcupine works—how molbits are designed and prepared, and how they are directly recognized by the software without an intermediate basecalling step.
Previous episodes
Generalized PCA for single-cell data with William Townes (#43)
Spectrum-preserving string sets and simplitigs with Amatur Rahman and Karel Břinda (#42)
Epidemic models with Kris Parag (#41)
Plasmid classification and binning with Sergio Arredondo-Alonso and Anita Schürch (#40)
Amplicon sequence variants and bias with Benjamin Callahan (#39)
Issues in legacy genomes with Luke Anderson-Trocmé (#38)
Causality and potential outcomes with Irineo Cabreros (#37)
scVI with Romain Lopez and Gabriel Misrachi (#36)
The role of the DNA shape in transcription factor binding with Hassan Samee (#35)
Power laws and T-cell receptors with Kristina Grigaityte (#34)
Genome assembly from long reads and Flye with Mikhail Kolmogorov (#33)
Deep tensor factorization and a pitfall for machine learning methods with Jacob Schreiber (#32)
Bioinformatics Contest 2019 with Alexey Sergushichev and Gennady Korotkevich (#31)
Bayesian inference of chromatin structure from Hi-C data with Simeon Carstens (#30)
Haplotype-aware genotyping from long reads with Trevor Pesout (#29)
Space-efficient variable-order Markov models with Fabio Cunial (#28)
Classification of CRISPR-induced mutations and CRISPRpic with HoJoon Lee and Seung Woo Cho (#27)
Feature selection, Relief and STIR with Trang Lê (#26)
Transposons and repeats with Kaushik Panda and Keith Slotkin (#25)
Read correction and Bcool with Antoine Limasset (#24)
RNA design, EteRNA and NEMO with Fernando Portela (#23)
smCounter2: somatic variant calling and UMIs with Chang Xu (#22)
Linear mixed models, GWAS, and lme4qtl with Andrey Ziyatdinov (#21)
Genome fingerprints with Gustavo Glusman (#19)
Bioinformatics Contest 2018 with Alexey Sergushichev and Ekaterina Vyahhi (#18)
Rarefaction, alpha diversity, and statistics with Amy Willis (#17)
Javier Quilez on what makes large sequencing projects successful (#16)
Optimal transport for single-cell expression data with Geoffrey Schiebinger (#15)
Generating functions for read mapping with Guillaume Filion (#14)
Bracken with Jennifer Lu (#13)
Modelling the immune system and C-ImmSim with Filippo Castiglione (#12)
Collective cell migration with Linus Schumacher (#11)
Spatially variable genes and SpatialDE with Valentine Svensson (#10)
Michael Tessler and Christopher Mason on 16S amplicon vs shotgun sequencing (#9)
Perfect k-mer hashing in Sailfish (#8)
Allele-specific expression (#6)
Relative data analysis and propr with Thom Quinn (#5)
ChIP-seq and GenoGAM with Georg Stricker and Julien Gagneur (#4)
miRNA target site prediction and seedVicious with Antonio Marco (#3)
Single-cell RNA sequencing with Aleksandra Kolodziejczyk (#2)