A Telomere Identification toolKit (tidk)

tidk is a toolkit to identify and visualise telomeric repeats for the Darwin Tree of Life genomes. tidk works especially well on chromosomal genomes, but can also work on PacBio HiFi reads as well (see the telomeric repeat database for many examples). There are a few modules in the tool, which may be useful to anyone investigating telomeric repeat sequences in a genome.

1. explore - tries to find the telomeric repeat unit in the genome.
2. find and search are essentially the same. They identify a repeat sequence in windows across the genome. find uses an in-built table of telomeric repeats, in search you supply your own.
3. plot does what is says on the tin, and plots the csv output of find or search as an SVG.

Install

The easiest way to install is through conda:

conda install -c bioconda tidk

Otherwise...

As with other Rust projects, you will have to complile yourself. Download rust, clone this repo, cd into it, and then run:

cargo install --path=.

To install into $PATH as tidk.

Usage

Below is some usage guidance. From 0.2.3 onwards there have been breaking changes to the CLI interface. They will be pointed out below, and in the release changelog.

Explore

tidk explore will attempt to find the simple telomeric repeat unit in the genome provided. It will report this repeat in its canonical form (e.g. TTAGG -> AACCT). Unlike previous versions, only a simple TSV is printed to STDOUT. Use the distance parameter to search only in a proportion of the chromosome arms. The default is 1% of the length of the chromosome either side, but feel free to change this. In particular with raw reads (PacBio), I'd recommend setting the distance flag to 0.5 (--distance 0.5 or --distance=0.5), to process the full length of each read.

For example: tidk explore --minimum 5 --maximum 12 fastas/iyBomHort1_1.20210303.curated_primary.fa > out.tsv searches the genome for repeats from length 5 to length 12 sequentially on the Bombus hortorum genome.

Use a range of kmer sizes to find potential telomeric repeats.
One of either length, or minimum and maximum must be specified.

Usage: tidk explore [OPTIONS] <FASTA>

Arguments:
  <FASTA>  The input fasta file

Options:
  -l, --length [<LENGTH>]        Length of substring
  -m, --minimum [<MINIMUM>]      Minimum length of substring [default: 5]
  -x, --maximum [<MAXIMUM>]      Maximum length of substring [default: 12]
  -t, --threshold [<THRESHOLD>]  Positions of repeats are only reported if they occur sequentially in a greater number than the threshold [default: 100]
      --distance [<DISTANCE>]    The distance from the end of the chromosome as a proportion of chromosome length. Must range from 0-0.5. [default: 0.01]
  -v, --verbose                  Print verbose output.
      --log                      Output a log file.
  -h, --help                     Print help
  -V, --version                  Print version

Find

tidk find will take an input clade, and match the known or putative telomeric repeat for that clade (or repeats plural) and search the genome. Now uses a custom curated telomeric repeat database. As more telomeric repeats are found and added, the dictionary of sequences used will increase.

Supply the name of a clade your organsim belongs to, and this submodule will find all telomeric repeat matches for that clade.

Usage: tidk find [OPTIONS] [FASTA]

Arguments:
  [FASTA]  The input fasta file

Options:
  -w, --window [<WINDOW>]  Window size to calculate telomeric repeat counts in [default: 10000]
  -c, --clade <CLADE>      The clade of organism to identify telomeres in [possible values: Accipitriformes, Actiniaria, Anura, Apiales, Aplousobranchia, Asterales, Buxales, Caprimulgiformes, Carangiformes, Carcharhiniformes, Cardiida, Carnivora, Caryophyllales, Cheilostomatida, Chiroptera, Chlamydomonadales, Coleoptera, Crassiclitellata, Cypriniformes, Eucoccidiorida, Fabales, Fagales, Forcipulatida, Hemiptera, Heteronemertea, Hirudinida, Hymenoptera, Hypnales, Labriformes, Lamiales, Lepidoptera, Malpighiales, Myrtales, Odonata, Orthoptera, Pectinida, Perciformes, Phlebobranchia, Phyllodocida, Plecoptera, Pleuronectiformes, Poales, Rodentia, Rosales, Salmoniformes, Sapindales, Solanales, Symphypleona, Syngnathiformes, Trichoptera, Trochida, Venerida]
  -o, --output <OUTPUT>    Output filename for the TSVs (without extension)
  -d, --dir <DIR>          Output directory to write files to
  -p, --print              Print a table of clades, along with their telomeric sequences
      --log                Output a log file
  -h, --help               Print help
  -V, --version            Print version

Search

tidk search will search the genome for an input string. If you know the telomeric repeat of your sequenced organism, this will find it and return counts of occurence in windows across the genome.

Search the input genome with a specific telomeric repeat search string.

Usage: tidk search [OPTIONS] --string <STRING> --output <OUTPUT> --dir <DIR> <FASTA>

Arguments:
  <FASTA>  The input fasta file

Options:
  -s, --string <STRING>          The DNA string to query the genome with
  -w, --window [<WINDOW>]        Window size to calculate telomeric repeat counts in [default: 10000]
  -o, --output <OUTPUT>          Output filename for the TSVs (without extension)
  -d, --dir <DIR>                Output directory to write files to
  -e, --extension [<EXTENSION>]  The extension, defining the output type of the file [default: tsv] [possible values: tsv, bedgraph]
      --log                      Output a log file
  -h, --help                     Print help
  -V, --version                  Print version

Plot

tidk plot will plot the output of tidk search.

SVG plot of TSV generated from tidk search.

Usage: tidk plot [OPTIONS] --tsv <TSV>

Options:
  -t, --tsv <TSV>          The input TSV file
      --height [<HEIGHT>]  The height of subplots (px). [default: 200]
  -w, --width [<WIDTH>]    The width of plot (px) [default: 1000]
  -o, --output [<OUTPUT>]  Output filename for the SVG (without extension) [default: tidk-plot]
  -h, --help               Print help
  -V, --version            Print version

As an example on the ol' Square Spot Rustic Xestia xanthographa:

tidk find -c lepidoptera -o Xes fastas/ilXesXant1_1.20201023.curated_primary.fa

tidk plot -t finder/Xes_telomeric_repeat_windows.tsv -o ilXes -h 120 -w 800

Cited by:

• Kurbessoian, Tania, et al. "In host evolution of Exophiala dermatitidis in cystic fibrosis lung micro-environment." BioRxiv (2022): 2022-09.
• Yin, Denghua, et al. "Gapless genome assembly of East Asian finless porpoise." Scientific Data 9.1 (2022): 765.
• Leonard, Guy, et al. "A genome sequence assembly of the phototactic and optogenetic model fungus Blastocladiella emersonii reveals a diversified nucleotide-cyclase repertoire." Genome Biology and Evolution 14.12 (2022): evac157.
• Edwards, Richard J., et al. "A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidii." BioRxiv (2022): 2022-04.

Omissions

Both tidk trim and tidk min have been removed from the latest version.