Tool:Tinybio Slackbot - a large language model slackbot for bioinformatics

Question

[Sasha]

Hi guys!

I'm launching a new Slackbot designed specifically to help with bioinformatics-focused questions in your workspace. I would love for folks to try it out and let me know how it works.

You can set this up in your workspace by clicking here: https://tinybio.slack.com/apps/A053URSLYKU-tinybio?tab=more_info

Or, you can join our community slack group here and play with the bot in our instance: https://join.slack.com/t/tinybiocommunity/shared_invite/zt-1uwwhw6gi-_r0PBFWzwgbs6YP8s_Dlvg

Would love any feedback as well. We're going to be rolling out a Discord version as well soon. See a simple example below. It really shines in helping QA with some of the issues that you may be having.

[Istvan Albert]

How is it different from typing the same into ChatGPT? And it does not take 2-3 minutes ...

Can you give me two variant callers?

Sure, variant callers are bioinformatics software tools used to identify variants (like SNPs and indels) from sequence data. Here are two commonly used variant callers:

GATK (Genome Analysis Toolkit): Developed by the Broad Institute, GATK is a well-known toolkit for the analysis of high-throughput sequencing data. It includes multiple tools, but is best known for its variant calling algorithms. One of the most commonly used workflows is the "Best Practices" pipeline for variant calling on DNA-seq data, which includes steps for alignment, removal of duplicate reads, indel realignment, base recalibration, and variant calling.

FreeBayes: This is another popular variant caller. FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.

FWIW I don't like either answer, the default variant caller everyone should start with is bcftools conceptually much simpler, faster and teaches the beginner (someone asking this question must be new at it) dealing with VCF files as well - which in the end is more important than the variant calling itself.

[Sasha]

Great question.

The base model had been modified to be more bioinformatics focused, provide code feedback, and has context windows that are focused on the most up to date code from the relevant toolsets! ChatGPT is a great product as well but this is modified to be more useful for QA cases as it has more context provided to it on the backend aside from the error itself.