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Please complete the survey below as follows.
- Division of Faculty Member (GI/Nutrition/Hepatology)
- Faculty Member (Ahmed M Moustafa)
- Type of teaching (Lectures/Discussions etc.)
- Date of Teaching (12-01-2023 or any other date during the workshop)
- Topic of Lecture (Microbial Genomics Journey Workshop-12 weeks)
- Your Position (put your position)
- Quality of this instructor (choose a value)
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We started this workshop with "Map your Microbial Genomics knowledge out". Knowledge mapping helps communicate information and solve complex problems. Now it is time to update your knowledge map with what we learnt in this workshop. Here is my version. You can access a powerpoint version of this Microbial genomics knowledge map here.
phastest PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is the successor to the PHAST and PHASTER prophage finding web servers. PHASTEST is available online at https://phastest.ca, as an API for programmatic queries, or as a Docker image for local installations. You can check publication here.
PlasmidFinder. This tool identifies plasmids in complete or draft sequenced isolates of bacteria. It can be accessed through this website or installed locally using docker. Instructions can be found here.
geNomad. A tool for Identification of mobile genetic elements. Its primary goal is to identify viruses and plasmids in sequencing data (isolates, metagenomes, and metatranscriptomes).
mamba create -n genomad -c conda-forge -c bioconda genomad
geNomad depends on a database that contains the profiles of the markers that are used to classify sequences, their taxonomic information, their functional annotation, etc. So, your first step is to download the database to your current directory or any other location on your computer
mamba activate genomad
genomad download-database .
The database will be contained within the genomad_db directory.
Using this K. pneumoniae genome GCF_009025895.1 as input. Generally, you can use any FASTA file containing nucleotide sequences as input. The tool will work for isolate genomes, metagenomes, and metatranscriptomes.
genomad end-to-end --cleanup --splits 8 GCF_009025895.1.fna.gz genomad_output genomad_db
The results will be written inside the genomad_output directory. Let's explore GCF_009025895.1_summary.tsv
Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.
CladeBreaker test the hypothesis of clonality by using the most similar genomes available in the database. If these genomes fail to break up the monophyly of the outbreak clade then this provides the strongest evidence possible for clonality.
Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.
Sunbeam is a pipeline written in snakemake by Kyle Bittinger team that simplifies and automates many of the steps in metagenomic sequencing analysis. It can be deployed on most Linux workstations and clusters. To read more, check out their paper in Microbiome.
- Programming for Biology Course at Cold Spring Harbor Laboratory.
- Instructed by Simon Prochnik, Circularis Biotech Inc. and Sofia Robb, Stowers Institute for Medical Research.
- Designed for lab biologists with little or no programming experience, this course will give students the bioinformatic sand scripting skills they need to derive biological insights from this abundance of data.
- The only prerequisite for the course is a strong commitment to learning basic UNIX and a scripting language.
- Lectures and problem sets from previous years are available online.
- They use Python and the course begins with one week of introductory coding, continues with practical topics in bioinformatics, with plenty of coding examples, and ends with a group coding project.