Getting Started

IsoTools is a python module for Long Read Transcriptome Sequencing (LRTS) analysis.

Key features:

• Import of LRTS bam files (aligned full length transcripts).

• Import of reference annotation in gff3/gtf format.

• Computation of quality control metrics.

• Annotation and classification of novel transcripts with biologically motivated classification scheme.

• Definition of alternative splicing events based on segment graphs.

• Detection of differential alternative splicing between samples and groups of samples.

• Data visualization.

Installation

The package can be installed with pip:

python3 -m pip install isotools

Usage

This code block demonstrates the basic file import with isoseq. For a more comprehensive real world example see the tutorial.

from  isotools import Transcriptome
import logging
logging.basicConfig(format='%(levelname)s:%(message)s', level=logging.INFO)
isoseq=Transcriptome.from_reference('reference_file.gff3.gz')
isoseq_bam_fn={'sample1':'isoseq_fn_s1.bam', 'sample2':'isoseq_fn_s2.bam'}
groups={'sample1':'control', 'sample2':'treatment'}
for sa,bam in isoseq_bam_fn.items():
    isoseq.add_sample_from_bam(bam, sample_name=sa, group=groups[sa])
isoseq.add_qc_metrics('genome.fa')
isoseq.make_index()
isoseq.add_filter()
isoseq.save('example_isotools.pkl')

Citation and feedback

• If you run into any issues, please use the github issues report feature.

• For feedback, please write me an email to lienhard@molgen.mpg.de.

• If you use isotools in your publication, please cite the following paper: IsoTools: a python toolbox for long-read transcriptome sequencing (in preparation)