Ani Ann's: Ani augmented Annotation of satellite arrays.
Ani Ann's is an a priori satellite detection and annotation software. Ani Ann's uses a matrix of Average Nucleotide Identity (Ani) values created by ModDotPlot to infer the location and type of satellites.
Note that Ani Ann's is currently under active development, and not all features are currently available.
git clone https://github.com/marbl/ModDotPlot.git
cd ModDotPlot
Although optional, setting up a virtual environment is recommended:
python -m venv venv
source venv/bin/activate
Once activated, you can install the required dependencies:
python -m pip install .
Currently, use of Ani Ann's is limited to detecting satellites and masking these regions. Classification of satellites, detection of Higher Order Repeats, and other metrics are not yet included.
Ani Ann's can be run with python src/anianns/anianns.py, or simply with the shortcut annotate:
annotate -h
Ani Ann's: Ani augmented Annotation of satellite arrays
options:
-h, --help show this help message and exit
-f FASTA [FASTA ...], --fasta FASTA [FASTA ...]
Path to input fasta file(s).
-b BAND, --band BAND Max height in Mbp of band. (default: 8.0)
-k KMER, --kmer KMER k-mer length (default: 21)
--overlap OVERLAP Percent overlap. Must be < 0.5. (default: 0.1)
--identity IDENTITY Identity threshold. (default: 86)
-o OUTPUT_DIR, --output-dir OUTPUT_DIR
Directory name for saving matrices and coordinate logs. Defaults to working directory. (default: None)
-w WINDOW, --window WINDOW
Window size of ModDotPlot. (default: 2000)
-m, --mask Create a masked fasta file. (default: False)
To both run repeat masker and annotation tools, simply run annotate -m/--mask.
-f / --fasta <file>
Fasta files to input. Multifasta files are accepted.
-k / --kmer <int>
K-mer size to use. This should be large enough to distinguish unique k-mers with enough specificity, but not too large that sensitivity is removed. Default: 21.
-o / --output-dir <string>
Name of output directory. Default is current working directory.
-id / --identity <int>
Minimum sequence identity cutoff threshold when running ModDotPlot. Default is 86. While it is possible to go as low as 50% sequence identity, anything below 80% is not recommended.
-w / --window <int>
Dotplot window size, or the number of bp contained within each pixel in a plot. This is proportional to the sensitivity of satellite detection (ie. lower is more accurate, at the expense of runtime). Default is 2000.
-b / --band <int * 1000000>
When creating dotplots, to save time, multiple plots of a certain size are used instead of the entire seqeunce length. This can be adjusted here (default: 8, or 8Mbp). Increasing this will improve detection of off-target satellites, at the expense of runtime.
--bed <str>
Name of bed file to output to. Default is anianns-output.bed.
For bug reports or general usage questions, please raise a GitHub issue, or email alex dot sweeten at nih dot gov