TECAT

TECAT (Telomere End Chromosome Assaying Tool)

Features

• Reference sequence analysis for de novo telomere motif discovery
• Highly customizable motif assignment for repettitive sequence matching
• Telomeric read identification with high fidelity
• Accurate telomere length analysis
• All step are parallelized
• Mapping telomeres back to reference for chromosome end-specific lengths

Installation

git clone https://github.com/jake-bioinfo/tecat.git
R CMD build tecat
R CMD INSTALL tecat

Quickstart

Workflow

Split fastq files

auto_split(fastq_file)

Find organism/sample specific telomere motifs

telomere_motif(reference_file)

Find telomeres in samples

telo_search(split_fastq_file_list)

Cut potential telomeres into rolling windows

sliding_window_parallel(telomere_file)

Calculate frequencies of windows

frequencies(windows)

Determine optimal thresholds

determine_threshold(telomere_frequencies)

optimal_thresholds(threshold_dataframe)

Truncate and map remainder read sequences

truncate_file(telomere_file)

map(truncated_reads, reference_file)

Plot results!

An in-depth vignette is included

vignettes/ONT_example_vignette.Rmd

License

GPL-3.0 License - see LICENSE file for details