De novo construction of isoforms from long-read data
Reason this release was yanked:
broken package
Project description
isONform - Reference-free isoform reconstruction from long read sequencing data
Table of contents
Installation
Via pip
pip install isONform
This command installs isONforms dependencies:
networkx
ordered-set
matplotlib
parasail
edlib
pyinstrument
namedtuple
recordclass
From github source
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Create a new environment for isONform (at least python 3.7 required):
conda create -n isonform python=3.10 pip
conda activate isonform
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Install isONcorrect and SPOA
pip install isONcorrect
conda install -c bioconda spoa
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Install other dependencies of isONform:
conda install networkx
pip install parasail
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clone this repository
Introduction
IsONform generates isoforms out of clustered and corrected long reads.
For this a graph is built up using the networkx api and different simplification strategies are applied to it, such as bubble popping and node merging.
The algorithm uses spoa to generate the final isoforms.
Running isONform
To run the algorithm:
python isONform_parallel.py --fastq_folder path/to/input/files --t <nr_cores> --outfolder /path/to/outfolder --split_wrt_batches
the isON-pipeline (isONclust, isONcorrect, isONform) can be run via:
./full_pipeline.sh <raw_reads.fq> <outfolder> <num_cores> <isONform_folder> <iso_abundance> <mode>
(Note that this requires pychopper, isONclust and isONcorrect to be installed)
Contact
If you encounter any problems, please raise an issue on the issues page, you can also contact the developer of this repository via: alexander.petri[at]math.su.se
Credits
Please cite [1] when using isONform.
- Petri, A. J., & Sahlin, K. (2023). isONform: reference-free transcriptome reconstruction from Oxford Nanopore data. Bioinformatics, 39(Supplement_1), i222-i231. https://academic.oup.com/bioinformatics/article/39/Supplement_1/i222/7210488 .
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