PI meeting notes 2024-07-03 To-Dos until next meeting: check if differences in ARG/BGC/AMP numbers are valid or are prone to biases from sampling/sequencing/assembly/contig length/identification tools or if we can/should normalize them to some parameters read publication of wastewater datasets (PDF)use figures as inspiration for own comparisons/analysis/interpretation of results check closely for any method biases (e.g. sample handling, sequencing, quality check...) go back to our own assembly from Louisa and check quality/stats fix remaining funcscan bugs (BGC summary (GECCO only in current summary?!) + stuffs on slack/Github)

graph TD subgraph metagenomic_profiling subgraph classification amino_acid_sequence_abundance nucleotide_sequence_abundance -->|dna_to_dna| genome nucleotide_sequence_abundance -->|dna_to_nuc_marker| gene amino_acid_sequence_abundance -->|dna_to_aa_marker| gene gene --> sequence_classification genome --> sequence_classification end

nf-enthusiasts collaborative notes 🌯 Feed me your notes! These have turned into Selina's personal notes, so while this feels powerful, please contribute :woman-bowing: Remind James to use box analogy :card_file_box: :-) 28.10.22 Setting up a new pipeline create conda environments on local machine and install nf-core tools

List of Microbiome Sciences Open Science Projects Project Status Author SPAAM NA James/Irina/Alex/Maxime/Tina AncientMetagenomeDir

Adding unit tests to nf-core pipelines with nf-test Introduction We should really add unit tests, and pytest is nice but a lot of overhead. Instead we will try with nf-test. This tutorial is based on experiences from the nf-test documentation and @nvnieuwk's testing. Install nf-test I've installed this with conda into my personal nf-core conda environment (containing nf-core tools, and nextflow).

<a href="https://www.nf-co.re/eager"><img src="https://github.com/nf-core/eager/raw/master/docs/images/nf-core_eager_logo_outline_drop.png" width="70%"><img></a> Introductory Tutorial James A. Fellows Yates 🦣 @jfy133@genomic.social / <img src="https://openmoji.org/data/color/svg/E045.svg" width=50> @jfy133 What is ancient DNA? Der Sarkissian et al. (2021) mSystems

nf-core/funcscan tutorial In this tutorial, we will guide you through how to set up a run for nf-core/funcscan almost from scratch! It will show you how to install nextflow, how to turn on and off different screening categories, and particular tools within each category. We will simulate having performed de novo assembly of two metagenomes, and wish to screen for antimicrobial resistance genes (ARG) and antimicrobial peptides (AMP). Prerequisites For this tutorial you will need basic command line experience.

Aesthetic If MPG: use just head or whole MPI one. Why not other logos (e.g. FSU?) otherwise just stick to Tübingen, can use space for QR code of the whole poster Make sure font size is equal throughout (Stick to three sizes, if possible - references/acknolwedgments excluded). Aims is bigger that th erest Stick to one font! (jut arial) -> methods seems to be a mix? Over-use of bolding causes you to zone out of it. Stick to itjust for headers (e.g. how you did in intro, that was very nice to emphasise the main points)

Paleobiotech Workshop Methods Nov. 12 2021 - MPI-EVA, Leipzig Task Three slides: 👩🏿‍🏫 Introduce your method to 🧱 Describe the biggest problem or obstacle