Micro binfie podcast

We go over tree visualizations!

* Microreact https://microreact.org/,https://www.phylocanvas.gl/

* grapetree https://github.com/achtman-lab/GrapeTree

* Auspice/NextStrain https://nextstrain.org/

* Taxonium https://taxonium.org/

* Itol: https://itol.embl.de/

* PhyloViz https://online.phyloviz.net/index

* Phandango https://jameshadfield.github.io/phandango/#/main

125 Kostas Konstantinidis returns to talk to us about ANI and metagenomics by Microbial Bioinformatics

We talk with Kostas! For more information please visit https://enve-omics.gatech.edu/

In this episode of the Micro Binfie Podcast, hosts Dr. Andrew Page and Dr. Lee Katz delve into the fascinating world of hash databases and their application in cgMLST (core genome Multilocus Sequence Typing) for microbial bioinformatics.

The discussion begins with the challenges faced by bioinformaticians due to siloed MLST databases across the globe, which hinder synchronization and effective genomic surveillance. To address these issues, the concept of using hash databases for allele identification is introduced. Hashing allows for the creation of unique identifiers for genetic sequences, enabling easier database synchronization without the need for extensive system support or resources.

Dr. Katz explains the principle of hashing and its application in genomics, where even a single nucleotide polymorphism (SNP) can result in a different hash, making it a perfect solution for distinguishing alleles. Various hashing algorithms, such as MD5 and SHA-256, are discussed, along with their advantages and potential risks of hash collisions. Despite these risks, the use of more complex hashes has been shown to significantly reduce the probability of such collisions.

The episode also explores practical aspects of implementing hash databases in bioinformatics software, highlighting the need for exact matching algorithms due to the nature of hashing. Existing tools like eToKi and upcoming software are mentioned as examples of applications that can utilize hash databases.

Furthermore, the conversation touches on the concept of sequence types in cgMLST and the challenges associated with naming and standardizing them in a decentralized database system. Alternatives like allele codes are mentioned, which could potentially simplify the representation of sequence types.

Finally, the potential for adopting this hashing approach within larger bioinformatics organizations like Phage or GMI is discussed, with an emphasis on the need for a standardized and community-supported framework to ensure the longevity and effectiveness of hash databases in microbial genomics.

This episode provides a comprehensive overview of how hash databases can revolutionize microbial genomics by solving long-standing issues of database synchronization and allele identification, paving the way for more efficient and collaborative genomic surveillance worldwide.

We discuss GAMBIT, software for accurately classifying bacteria and eukaryotes using a targeted k-mer based approach.

GAMBIT software: https://github.com/gambit-suite/gambit

GAMBIT suite: https://github.com/gambit-suite

GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.

https://doi.org/10.1371/journal.pone.0277575

TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization

https://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2023.1198213/full

In this episode, Andrew Page and Lee Katz continue their conversation with Titus Brown, diving deeper into his work on k-mers, Sourmash, and open source software development:

Topics discussed:

K-mers for analyzing sequencing data, and how Sourmash builds on MinHash

How Sourmash handles k-mers for metagenomic comparisons vs. MASH

The modhash and bottom sketch approaches used in Sourmash

Dealing with sequencing errors and noise in k-mer data

Sourmash as a reference-based method, and applications for metagenomics

Titus' focus on building reusable libraries and APIs vs one-off tools

Recruiting collaborators through "nerd sniping" with interesting problems

The open source philosophy that motivates Titus' software work

Overall, the conversation provides insight into Titus' approach to bioinformatics software through iterating quickly, focusing on usability, and building open source tools.

Papers:

Spacegraphcats - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4

Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2

IBD exploration - https://dib-lab.github.io/2021-paper-ibd/

In this final episode with Titus Brown, the conversation focuses on his work scaling metagenomic search with Sourmash:

An overview of what Sourmash does - sketching and comparing large k-mer datasets

How the sampling approach enables analyses like containment estimation

Exciting capabilities of the Branchwater tool for multi-threaded real-time SRA search

Scaling to search across millions of metagenomes in seconds with WebAssembly

Potential public health applications for tracking and sourcing pathogens

Important caveats around resolution limits and need for follow-up analyses

Ongoing work to characterize the technique's specificity and sensitivity

Overall, this episode highlights the massive scaling Sourmash enables for metagenomic search, and the potential use cases in public health, while acknowledging current limitations and uncertainties. Titus emphasizes the need to precisely convey what bioinformatic tools can and cannot do as research continues.

Papers:

Spacegraphcats - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4

Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2

IBD exploration - https://dib-lab.github.io/2021-paper-ibd/

In this episode, Andrew Page and Lee Katz continue their chat with Titus Brown, focusing on taxonomy assignment in metagenomics:

Topics discussed:

Dealing with contamination and low quality genomes in reference databases

Sourmash as a versatile search tool, not a curated database

The need for high confidence in taxonomic assignment in public health

Most microbial assignment tools have low specificity or sensitivity

Possible ways to achieve perfect species classification (in theory)

The challenges around defining species based on small genomic differences

Interesting cryptography concept of 'unicity' distance for classification

Conveying the nuances and uncertainties in taxonomic assignment

The conversation highlights the difficulties around taxonomic classification, especially at the species level, but explores ideas for improving accuracy. Overall it emphasizes the complexities of biology and need for transparent conveyance of uncertainties.

Papers:

Spacegraphcats - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4

Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2

IBD exploration - https://dib-lab.github.io/2021-paper-ibd/

Andrew, Nabil, and Lee react to the bioinformatics and the science overall in the 1993 film Jurassic Park.

We looked at these YouTube clips:

* https://youtu.be/mDTaykXudVI?si=I5aiUdBGStpIKHVC

* https://youtu.be/RLz5Api676Y?si=D6nps33O42Fmk4Ac

* https://youtu.be/0Nz8YrCC9X8?si=KNwkeFoS6Bu4LOpv

* https://youtu.be/dxIPcbmo1_U?si=TOBw5AONYVCW0JzV

* https://youtu.be/m1lc8GwBKFE?si=rj7Oiq51l2_dB6ro

More information on the secret tattoo here: https://underunderstood.com/podcast/episode/jeff-goldblums-secret-tattoo-jurassic-park-ian-malcolm/

In this episode of the Micro Binfie Podcast, Andrew Page and Lee Katz interview Titus Brown about his journey from studying math and physics as an undergrad to becoming a bioinformatician focusing on metagenomics and software development.

Topics discussed:

Titus' background in math, physics, digital evolution research, and developmental biology

His transition into bioinformatics to analyze the influx of genomic data in the 1990s

Developing early tools for comparative genomics and sequence analysis

The philosophy of creating usable software with good documentation

Work on transcriptomics, metagenomics, and k-mers at Michigan State

Digital normalization and dealing with large sequencing datasets

Moving to UC Davis and continuing work on metagenomics and software like khmer and sourmash

Thoughts on challenges around data reuse and accessibility in science.

Papers:

Spacegraphcats - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4

Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2

IBD exploration - https://dib-lab.github.io/2021-paper-ibd/