This repository contains the scripts, pipelines, input and output files used for the analysis of Trans-splicing Acceptor Sites (TAS) and dinucleotide composition in trypanosomatid genomes.
The analyses were performed independently for three parasites:
- Trypanosoma cruzi
- Trypanosoma brucei
- Leishmania major
This work is associated with the following manuscript (pre-print):
bioRxiv: https://www.biorxiv.org/content/10.1101/2025.07.08.663533v1
data/# Input genomic data and annotation files for each TriTryp- Genome annotation files (GFF)
- FASTA files
- TAS predictions from UTRme
- Single and multi-copy coordinates
output/# Partial results generated by the analyses- Quality control plots from fastqc
- 2D plots generated from genomic alignments
- Alignment summary tables and reports
scripts/# Analysis pipelines and parasite-specific scripts- Analysis of regions near TAS
- Dinucleotide analysis
tools/# Standalone helper scripts- Software and tools used in the analysis
- Script for length distribution histograms
- Script for generating bigwig files