Assemblytics is available online at http://assemblytics.com
:warning: Assemblytics is pretty outdated at this point, made around 2015 when no other assembly-based variant callers were available and I needed one for my own research. Since then the use of genome assembly has exploded and many more tools are available for downstream variant calling from assemblies, like SVIM-asm and SyRI. Given it's been 8 years since I published Assemblytics, and I haven't worked with genome assemblies since then, I'm not in a great position to answer your questions, compare Assemblytics' results to other tools, or provide scientific support, but I have done my best to keep it up and running online for those who continue to rely on it. Feel free to use the github issues here to share your favorite alternative assembly-based variant callers. Good luck with your research! 🙏 Maria
Please cite our paper in Bioinformatics: http://www.ncbi.nlm.nih.gov/pubmed/27318204
The preprint is still freely available on the BioRxiv: https://www.biorxiv.org/content/10.1101/044925v1
There are three ways to use Assemblytics:
scripts/
directory. See instructions below.IMPORTANT: Assemblytics has been configured to work only with MUMmer3 and using the following alignment instructions. Running Assemblytics with any other delta file as input may give errors or miscallibrated results.
Upload a delta file to analyze alignments of an assembly to another assembly or a reference genome
Download and install MUMmer 3
Align your assembly to a reference genome using nucmer (from MUMmer package)
nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT
# Settings above are important for unique anchor filtering to work correctly in Assemblytics.
Consult the MUMmer 3 manual if you encounter problems.
Optional: Gzip the delta file to speed up upload (usually 2-4X faster)
gzip OUT.delta
Then use the OUT.delta.gz file for upload.
Upload the .delta or delta.gz file (view example) to Assemblytics
Important: Use only contigs rather than scaffolds from the assembly. This will prevent false positives when the number of Ns in the scaffolded sequence does not match perfectly to the distance in the reference.
The unique sequence length required represents an anchor for determining if a sequence is unique enough to safely call variants from, which is an alternative to the mapping quality filter for read alignment.
If you prefer to run Assemblytics from the command-line the scripts/ directory contains all the code you need, from unique anchor filtering and calling variants to creating the output plots and summary tables.
To run Assemblytics on the command-line, keep all the scripts together inside the scripts/
directory, either in your PATH or anywhere else you like, and make them all executable:
chmod a+x scripts/Assemblytics*
Keeping the scripts together in the same folder will allow the main Assemblytics
script to call all the other scripts that do filtering, analysis, indexing, and plotting.
Follow the instructions at http://assemblytics.com for how to prepare your data and get a delta file for Assemblytics.
Then run Assemblytics:
scripts/Assemblytics <delta_file> <output_prefix> <unique_anchor_length> <min_variant_size> <max_variant_size>
The whole web application can be downloaded and run locally, utilizing the graphical user interface and giving the added benefit of the interactive dot plot which is only available in the web version and cannot run from the CLI.
Notes for installation:
assemblytics
, to make the .htaccess
file point the server correctly to the public/
folder, where the index.php and other pages and web app resources are located.