andro

andro is a reference-guided command line tool for finding and annotating human ribosomal DNA (rDNA) units in FASTA sequences. It is built around the KY962518-ROT reference, reports annotations in BED format, and can optionally generate dotplots for detected units.

The tool was developed as part of a bachelor's thesis project and is intended for exploratory analysis of human rDNA-containing assemblies.

Installation

Install the latest release from PyPI:

pip install andro

Or install from a local clone:

git clone https://github.com/dmelkovic/andro.git
cd andro
pip install .

Basic usage

Run andro with a FASTA file:

andro example.fa

By default, results are written to standard output in BED format. To write the annotations to a file:

andro example.fa -o annotations.bed

To generate a dotplot for each reported unit:

andro example.fa --plot ref --dir plots

Display all available options with:

andro --help

What andro reports

Given a FASTA file with one or more records, andro will:

• find 5.8S rDNA candidates and extend them to full 45S regions when possible
• find rDNA units anchored by detected 45S regions
• extend detected 45S regions to full rDNA units when the surrounding sequence supports it
• annotate major rDNA features
• write annotations in BED format
• optionally generate dotplots for each reported unit

Design choices and limitations

Forward orientation

andro searches for rDNA units in the forward orientation relative to the KY962518-ROT reference. This keeps annotation coordinates consistent with the ordered 45S and IGS model used internally.

If an assembly contains rDNA arrays in the reverse-complemented orientation, run andro on a reverse-complemented copy of that FASTA record as a separate input.

Complete 45S regions by default

By default, andro reports only units where a complete 45S region is found. If a substantial part of the 45S region is missing, the sequence is not reported as an rDNA unit in the default mode.

The --partial option enables reporting of incomplete units. Partial-unit annotation is experimental: regions shorter than approximately 2500 bp are not reported, and incomplete annotations should be reviewed manually before being used downstream.

Reference

andro includes the KY962518-ROT reference sequence used for detection and annotation. Results should be interpreted relative to that reference and the feature model encoded in the package.

License

andro is distributed under the MIT License. See LICENSE for details.

Issues

Please report bugs and unexpected results at:

https://github.com/dmelkovic/andro/issues