RADIAN
RNA lAnguage informeD decodIng of nAnopore sigNals
Overview
Nanopore direct RNA basecaller that utilises a model of mRNA language.
Since RNA is always sequenced from the 3' to 5' direction, nanopore signals implicitly encode the nucleotide biases in mRNA. This basecaller uses a probabilistic model of human mRNA language to guide basecalling when the signal prediction is ambiguous. The mRNA model is incorporated in a modified CTC beam search decoding algorithm.
Preprint: https://www.biorxiv.org/content/10.1101/2022.10.19.512968v1
Installation
cd <path/to/radian>
pip install --upgrade pip
pip install -r requirements.txt
tar -xvzf radian/models/rnamodel_12mer_pc.tar.gz
Command structure
usage: basecall.py [-h] fast5_dir fasta_dir [--local] [--chunk-len] [--step-size]
[--batch-size] [--outlier-clip] [--rna-model]
[--sig-model] [--sig-config] [--beam-width]
[--decode-type] [--sig-threshold]
[--rna-threshold] [--context-len]
positional arguments:
fast5_dir Directory of single/multi fast5 files.
fasta_dir Directory to output fasta files.
optional arguments:
-h, --help
--local
--chunk-len
--step-size
--batch-size
--outlier-clip
--rna-model
--sig-model
--sig-config
--beam-width
--decode-type {global,chunk}
--sig-threshold
--rna-threshold
--context-len
Example usage
We provide a fast5 file containing 5 reads for testing in data/reads.fast5.
To basecall the single or multi-fast5 file(s) in and output fasta to <out_dir>:
cd radian
mkdir out_dir
python3 basecall.py data out_dir