Assembly of Phylogenomic Datasets from High-Throughput Sequencing Data

Documentation: https://edgardomortiz.github.io/captus.docs

INSTALLATION

Using conda/mamba (recommended)

Captus is available as a conda package. If you have conda or mamba installed, you can easily create a new environment and install Captus with all dependencies using the following command:

Linux:

conda create -n captus -c bioconda -c conda-forge captus

or

mamba create -n captus -c bioconda -c conda-forge captus

Mac computers with Intel processors:

conda create -n captus -c bioconda -c conda-forge captus megahit=1.2.9=hfbae3c0_0

or

mamba create -n captus -c bioconda -c conda-forge captus megahit=1.2.9=hfbae3c0_0

Mac computers with Apple silicon (M processors):

conda create --platform osx-64 -n captus -c bioconda -c conda-forge captus megahit=1.2.9=hfbae3c0_0 mmseqs2=16.747c6

or

mamba create --platform osx-64 -n captus -c bioconda -c conda-forge captus megahit=1.2.9=hfbae3c0_0 mmseqs2=16.747c6

Warning

The following programs provided by bioconda contain bugs or compilation errors, if you notice any problem try re-installing a valid version:

• BBTools v39.7X: use versions <= 39.52 or >= 39.80 (add bbmap=39.52 to the installation commands, or run conda install -c bioconda bbmap=39.52 with your Captus environment activated if Captus is already installed)
• Salmon v1.11.4: use version 1.10.3 (add salmon=1.10.3 to the installation commands, or run conda install -c bioconda salmon=1.10.3 with your Captus environment activated if Captus is already installed)
• MAFFT v7.525: use version 7.526 (add mafft=7.526 to the installation commands, or run conda install -c conda-forge mafft=7.526 with your Captus environment activated if Captus is already installed)

Then check that Captus was correctly installed:

conda activate captus
captus -h

If the program was correctly installed, you will see the following help message:

usage: captus command [options]

Captus 1.6.5: Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Captus-assembly commands:
  command     Program commands (in typical order of execution)
                clean = Trim adaptors and quality filter reads with BBTools,
                        run FastQC on the raw and cleaned reads
                assemble = Perform de novo assembly with MEGAHIT and estimate
                           contig depth of coverage with Salmon. Assembling
                           reads that were cleaned with the 'clean' command is
                           recommended, but reads cleaned elsewhere are also
                           allowed
                extract = Recover targeted markers with BLAT and Scipio:
                          Extracting markers from the assembly obtained with
                          the 'assemble' command is recommended, but any other
                          assemblies in FASTA format are also allowed
                align = Align extracted markers across samples with MAFFT or
                        MUSCLE: Marker alignment depends on the directory
                        structure created by the 'extract' command. This step
                        also performs paralog filtering and alignment trimming
                        using TAPER and ClipKIT

Help:
  -h, --help  Show this help message and exit
  --version   Show Captus' version number

For help on a particular command: captus_assembly command -h

Manual installation

If you are unable to use conda/mamba for any reason, you will need to install all dependencies manually. Please refer to the documentation for details.

USAGE

Documentation and tutorials are available at https://edgardomortiz.github.io/captus.docs

Tip

Extract BUSCO

Since v1.0.1, Captus supports the use of any BUSCO lineage dataset as reference targets for extraction. Just download one of the .tar.gz files from https://busco-data.ezlab.org/v5/data/lineages and provide the path to captus extract.

For example:

captus extract -a 02_assemblies -n ~/Downloads/aves_odb10.2021-02-19.tar.gz

CITATION

Ortiz, E.M., A. Höwener, G. Shigita, M. Raza, O. Maurin, A. Zuntini, F. Forest, W.J. Baker, H. Schaefer. (2023). A novel phylogenomics pipeline reveals complex pattern of reticulate evolution in Cucurbitales. bioRxiv https://doi.org/10.1101/2023.10.27.564367