🧬 Assemblycomparator2 "asscom2" is a genomes-to-report pipeline. It accepts prokaryotic (bacterial and archaeal) genomic assemblies and compares them in many different ways.
🦠 Being designed to analyze assemblies of both isolates and metagenomes (MAGs), it is useful for anyone working with microbial genomics.
💾 Installing Assemblycomparator2 on your system gives you access to many powerful state-of-the-art tools for analysis of prokaryotic genomes which will accelerate your research. It is easy to use and can be used by non-bioinformaticians.
👩🔬 Assemblycomparator2 integrates several analyses that yield scientific results about genomic assemblies on several levels: Quality control, annotation, function and species calling as well as comparative analyses like computation of core/pan genomes and phylogenetics.
🐍 Assemblycomparator2 works by calling a Snakemake workflow that can be easily modified to use different parameters for the underlying tools.
📙 Central results are dynamically integrated in a compact portable report .html-document. It can be browsed in any web browser and can be easily shared as a single file. This report is generated even if some jobs in the pipeline fail. See examples.
🧑💻 Assemblycomparator2 can be run either on a local workstation (recommended >= 64GiB RAM), or a HPC (high performance computing) cluster. Both Apptainer/Singularity/Docker images and conda environment definitions are available for all dependent software to run.
The comprehensible documentation is available at assemblycomparator2.readthedocs.org.
Please log any issues you have in the issues tab of the repository.
Development is active and will continue. We're actively looking for collaborators to join and synergize this project. Pull requests are warmly encouraged.
Assemblycomparator2 genomes to report pipeline. Copyright (C) 2024 Carl M. Kobel GNU GPL v3