HTvertebrates

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scripts used to analyse horizontal transfer and evolution of transposable elements in 307 vertebrate species

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# HTvertebrates

Scripts used in "Horizontal transfer and evolution of transposable elements in vertebrates" by Hua-Hao Zhang, Jean Peccoud, Min-Rui-Xuan Xu, Xiao-Gu Zhang, Clément Gilbert (doi: 10.1038/s41467-020-15149-4).

These scripts are publicly available to indicate how parts of the analysis were automated. There is no guaranty regarding their use. 
For those who want to use the pipeline, see below:

## Requirements
- [R](https://cran.r-project.org) 3.4+ with the following packages:
  - [data.table](https://cran.r-project.org/web/packages/data.table/) 1.11.4
  - [stringi](https://cran.r-project.org/web/packages/stringi/) 1.2.4
  - [matrixStats](https://cran.r-project.org/web/packages/matrixStats/) 0.54
  - [igraph](https://cran.r-project.org/web/packages/igraph/) 1.2.4.1
  - [ape](https://cran.r-project.org/web/packages/ape/) 5.1
  - [seqinr](https://cran.r-project.org/web/packages/seqinr/) 3.4-5
  - [Biostrings](https://bioconductor.org/packages/release/bioc/html/Biostrings.html) 2.52
  - [RColorBrewer](https://cran.r-project.org/web/packages/RColorBrewer/) 1.1-2

(If not found, these packages are installed automatically by the pipeline.)

- [RepeatModeler](http://www.repeatmasker.org/RepeatModeler/) 1.0.10
- [RepeatMasker](http://www.repeatmasker.org/RMDownload.html) 4.0.7
- [BUSCO](https://gitlab.com/ezlab/busco) 3.0.1
- [ncbi blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) 2.6.0
- [diamond](https://github.com/bbuchfink/diamond) 0.9.19
- [seqtk](https://github.com/lh3/seqtk) 1.2-r94 
- [Slurm Workload Manager](https://slurm.schedmd.com/download.html) 17.11.7

The pipeline was not tested with other versions of the above programs, but more recent versions probably work.

Hardware requirements: a linux cluster with
- ≥200 CPUs
- ≥0.5 TB of system memory
- ≥2 TB of free hard drive space 
- an internet connection to download the genome sequences (>10 MB/s is recommended).

On this hardware, the pipeline should take 1-2 months to complete.

## File description
The R scripts whose names start with numbers performed successive stages of the analysis. The purpose of each script is described by comments at the beginning of the script.

- `HTvFunctions.R` contains functions required for the other scripts and is sourced automatically.
- `circularPlots.R` contains functions used to draw Figure 2 of the paper. 
- The remaining scripts are launched via `Rscript` (for long, CPU-intensive tasks) from the scripts whose names start with numbers.

The files in directory `additonal_files` are required by the scripts:
- `supplementary-data1-genomes_and_accessions.txt` gives general information about the genomes and is used to download genomes sequences from ncbi.
- `ftp_links.txt` contains URL to the genome sequences, also used to download genome sequences.
- `timetree.nwk` is the timetree (newick format) used through the analysis.
- `namedClades.txt` is a table of major vertebrate clades in this tree, with their names and color codes used to make some of the paper's figures (these figures are generated by the scripts).
- `superF.txt` makes the correspondance between repeatModeler family codes (first column), TE class (2nd column) and more common TE superfamily names (3rd column). It is used in stages 15 and 16.
- `supplementary-data3-TEcomposition_per_species.txt` is generatd by the scripts and is provided with the paper, but we also provide it here if to facilitate the reproduction of the results.

The directory `demo_TeKaKs` is provided to demo the script `TEKaKs.R` (see `Demonstration of TEKaKs.R` below), but is not required to run the pipeline.

## Installation
In a bash-compatible terminal that can execute git, paste
```
git clone https://github.com/jeanlain/HTvertebrates.git
cd HTvertebrates/
```

Alternatively, download https://github.com/jeanlain/HTvertebrates/archive/master.zip and uncompress the zip file.

## Usage
Run R scripts whose name start with numbers in the corresponding order, always from the `HTvertebrates/` directory, which should be set as the working directory.
We recommand running these scripts (except stage 1) in interactive mode.

Adapting this pipeline to other datasets, hardware configuration, and automating all procedures require modifications to the code. Some parts of the analysis were not automated.

### Demonstration of TEKaKs.R to compute pairwise Ka and Ks on tranposable elements
We detail how to run `TEKaKs.R` on a demo dataset, but we remind that this script (as all others) is not intended for use in any other context than the study associated with the paper.

This script computes Ka, Ks, and well as overall molecular distances on pairs of homologous transposable elements (TEs), based on HSPs between these TEs and on HSPs between TEs and proteins (HSPs are not generated by this script). See the paper's method section for a description of the approach.

The hardware requirement for this demo is a Mac/Unix/Linux computer with at last 8GB of RAM, 1GB of free hard drive space, and which is able to execute R 3.4+ in a terminal. A Windows computer cannot run the script as some R functions are not supported under windows (namely those of the `parallel` R package).

A Mac computer may have issues installing the `igraph` R package from sources, as macOS lacks a fortran compiler. However, the `igraph` package may be installed manually by specifying NOT to install packages from sources (which is not possible to do via `Rscript`).

The other programs mentioned in the `Requirements` section need not be installed for this demo.

The `demo_TeKaKs/` directory must be immediately within the `HTvertebrates/` directory. It contains the following:
- `TEhitFile.txt` is a file of TE-TE HSPs in typical blast tabular format, but only listing sequence names and HSP coordinates.
- `blastxFile.txt` is a tabular file of TE-protein HSPs. The fields indicate the TE sequence name, start and end coordinates of the HSP on this sequence (where start < end), start coordinate of the HSP on the protein and whether the TE sequence in aligned on the protein in reverse direction.
- `fastaFile.fas` is a fasta file of the TE sequences whose names are in the two aforementioned files.

The nature of these files is also explained by comments in `TEKaKs.R`.

To run the demo, paste the following in the terminal session that you used to install the pipeline:
```
Rscript TEKaKs.R demo_TeKaKs/TEhitFile.txt demo_TeKaKs/blastxFile.txt demo_TeKaKs/fastaFile.fas demo_TeKaKs/output 2
```
where `demo_TeKaKs/output` is the output folder (automatically created) and `2` is the number of CPUs to use.

The script should run in less than 5 minutes on a standard desktop PC.

Results will be found in `demo_TeKaKs/output/allKaKs.txt`. This tabular file contains the following fields:
- `hit` is an identifier for each HSP, which corresponds to the row index of each HSP in `TEhitFile.txt`.
- `ka`, `ks`, `vka` and `vks` are the results of Ka and Ks computations (see the `kaks()` function of `seqinr`), 
- `length` is the length of the alignment on which the above were computed.
- `nMut` is the number of substitutions in this alignment.
- `K80distance` and `rawDistance` are molecular distances (according to Kimura 1980 or without any correction) between sequences in the HSP. These are computed before any of the processing required for the Ka Ks computations (the removal of certain nucleotides and codons, see the method section of the paper).

## Output of the pipeline
More than 1TB of intermediate files are generated.
The final output corresponds to results of the publication (please see the publication for their description).
- `Figure2.pdf`, `Figure3.pdf` and `Figure4.pdf` are produced at stages 14, 15 and 16 respectively. They correspond to figures of the main text
- `FigureS1.pdf` is generated at stage 5. It corresponds to supplementary figure 1.
- `FigureS2.pdf` is generated at stage 11. It corresponds to supplementary figure 2.
- `FigureS[3-6].pdf` are generated at stage 16. They corresponds to supplementary figures 3-6.
- `tableS1.txt` is generated at stage 15. It corresponds to supplementary table 1.
- `tableS2.txt` is generated at stage 16. It corresponds to supplementary table 2.
- `supplementary-data3-TEcomposition_per_species.txt` is generated at stage 2. 
- `supplementary-data4-retained_hits.txt` is generated stage 12.

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