Assemblytics is available online at http://assemblytics.com

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:

1. Use the hosted online version at http://assemblytics.com. This is the easiest option.
2. Run it from the command-line. For this you need only the contents of the scripts/ directory. See instructions below.
3. Run the full web app from a local server. 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

1. Download and install MUMmer 3
2. 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.

3. 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.

4. 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.

• R
  • ggplot2
  • plyr
  • RColorBrewer
  • scales
• Python
  • argparse
  • numpy

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:

• Use a local server like Apache and follow the instructions there.
• Clone this repository into a folder called 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.
• Make sure to open up permissions in user_uploads and user_data so the webserver can read and write there.
• It does not contain the examples as some of these are huge files.