Tutorial: SemiBin2

tl;dr: Learn how to use SemiBin from the original developers. In particular, we will see how to run SemiBin on a set of of human gut samples with different binning modes.

Prerequisites

What you should know/be able to do before the tutorial:

• You should know what a contig and BAM file is.
• You should be able to run programmes on the command line
• You should be able to install SemiBin. You can see the details from How to install.

You will also be sent some information a few days before the tutorial with both the signup links & and some requests to prepare for the event. You should expect to spend some time (10-15 minutes) installing the software and downloading the tutorial data.

SIGN UP LINK

Learning objectives

• What is metagenomic binning?
• The basic ideas behind SemiBin2.
• How to get MAGs from SemiBin2 with different binning modes.
• We will not cover functional analysis of MAGs.

Location & Schedule

Date: 23rd October, 2023 @ 21h30 UTC (this is 5.30pm EDT/2.30pm PDT; morning of the 24th in Australia, check your timezone)

Location: Zoom & Discord (links will be sent to registered participants)

Background information

• SemiBin webpage: https://semibin.rtfd.io/
• SemiBin manuscripts: Pan et al. A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments, in Nature Communications (2022); and Pan et al. SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing, in Bioinformatics (2023).