clinker

Both cblaster and clinker can now be used without installation on the CAGECAT webserver.

Gene cluster comparison figure generator

What is it?

clinker is a pipeline for easily generating publication-quality gene cluster comparison figures.

Given a set of GenBank files, clinker will automatically extract protein translations, perform global alignments between sequences in each cluster, determine the optimal display order based on cluster similarity, and generate an interactive visualisation (using clustermap.js) that can be extensively tweaked before being exported as an SVG file.

A note on scope:

clinker was designed primarily as a simple way to visualise groups of homologous biosynthetic gene clusters, which are typically small genomic regions with not many genes (as in the example GIF). It performs pairwise alignments of all genes in all input files using the aligner built into BioPython, then generates an interactive SVG document in the browser. The alignment stage will scale very poorly to multiple genomes with many genes, and the resulting visualisation will also be very slow given how many SVG elements it will contain. If you are looking to align entire genomes, you will likely be better served using tools built for that purpose (e.g. Cactus).

Installation

clinker can be installed directly through pip:

pip install clinker

By cloning the source code from GitHub:

git clone https://github.com/gamcil/clinker.git cd clinker pip install .

Or, through conda:

conda create -n clinker -c conda-forge -c bioconda clinker-py conda activate clinker

Citation

If you found clinker useful, please cite: clinker & clustermap.js: Automatic generation of gene cluster comparison figures. Gilchrist, C.L.M., Chooi, Y.-H., 2020. Bioinformatics. doi: https://doi.org/10.1093/bioinformatics/btab007

Usage

Running clinker can be as simple as:

clinker clusters/*.gbk

This will read in all GenBank files inside the folder, align them, and print the alignments to the terminal. To generate the visualisation, use the -p/--plot argument:

clinker clusters/*.gbk -p <optional: file name to save static HTML>

clinker can also parse GFF3 files:

clinker cluster1.gff3 cluster2.gff3 -p

Note: a corresponding FASTA file of the same name (extensions ".fa", ".fsa", ".fna", ".fasta" or ".faa") must be found in the same directory as the GFF3, i.e. cluster1.fa and cluster2.fa.

See -h/--help for more information:

``` usage: clinker [-h] [--version] [-r RANGES [RANGES ...]] [-gf GENE_FUNCTIONS] [-na] [-i IDENTITY] [-j JOBS] [-s SESSION] [-ji JSON_INDENT] [-f] [-o OUTPUT] [-p [PLOT]] [-dl DELIMITER] [-dc DECIMALS] [-hl] [-ha] [-mo MATRIX_OUT] [-ufo] [files ...]

clinker: Automatic creation of publication-ready gene cluster comparison figures.

clinker generates gene cluster comparison figures from GenBank files. It performs pairwise local or global alignments between every sequence in every unique pair of clusters and generates interactive, to-scale comparison figures using the clustermap.js library.

optional arguments: -h, --help show this help message and exit --version show program's version number and exit

Input options: files Gene cluster GenBank files -r RANGES [RANGES ...], --ranges RANGES [RANGES ...] Scaffold extraction ranges. If a range is specified, only features within the range will be extracted from the scaffold. Ranges should be formatted like: scaffold:start-end (e.g. scaffold1:15000-40000) -gf GENEFUNCTIONS, --genefunctions GENEFUNCTIONS 2-column CSV file containing gene functions, used to build gene groups from same function instead of sequence similarity (e.g. GENE_001,PKS-NRPS).

Alignment options: -na, --no_align Do not align clusters -i IDENTITY, --identity IDENTITY Minimum alignment sequence identity [default: 0.3] -j JOBS, --jobs JOBS Number of alignments to run in parallel (0 to use the number of CPUs) [default: 0]

Output options: -s SESSION, --session SESSION Path to clinker session -ji JSONINDENT, --jsonindent JSONINDENT Number of spaces to indent JSON [default: none] -f, --force Overwrite previous output file -o OUTPUT, --output OUTPUT Save alignments to file -p [PLOT], --plot [PLOT] Plot cluster alignments using clustermap.js. If a path is given, clinker will generate a portable HTML file at that path. Otherwise, the plot will be served dynamically using Python's HTTP server. -dl DELIMITER, --delimiter DELIMITER Character to delimit output by [default: human readable] -dc DECIMALS, --decimals DECIMALS Number of decimal places in output [default: 2] -hl, --hidelinkheaders Hide alignment column headers -ha, --hidealnheaders Hide alignment cluster name headers -mo MATRIXOUT, --matrixout MATRIXOUT Save cluster similarity matrix to file

Visualisation options: -ufo, --usefileorder Display clusters in order of input files

Example usage

Align clusters, plot results and print scores to screen: $ clinker files/*.gbk

Only save gene-gene links when identity is over 50%: $ clinker files/*.gbk -i 0.5

Save an alignment session for later: $ clinker files/*.gbk -s session.json

Save alignments to file, in comma-delimited format, with 4 decimal places: $ clinker files/*.gbk -o alignments.csv -dl "," -dc 4

Generate visualisation: $ clinker files/*.gbk -p

Save visualisation as a static HTML document: $ clinker files/*.gbk -p plot.html

Cameron Gilchrist, 2020 ```

Defining gene groups by function

By default, clinker automatically assigns a name and colour for each group of homologous genes. You can instead pre-assign names (i.e. functions) using the -gf/--gene_functions argument, which takes a 2-column comma-separated file like:

GENE_001,Cytochrome P450 GENE_002,Cytochrome P450 GENE_003,Methyltransferase GENE_004,Methyltransferase

This will generate two groups, Cytochrome P450 (GENE001 and 002), and Methyltransferase (GENE003, GENE_004). If there any other homologous genes are identified, they will automatically be added to these groups.

As of clinker v0.0.28, you can now specify colours for genes defined by the -gf/--gene_functions argument. To do this, use the -cm/--colour_map argument which also takes a 2-column CSV file containing the group name and hexadecimal colour code like:

Cytochrome P450,#FF0000 Methyltransferase,#0000FF