Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

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

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Warning

VERY IMPORTANT FOR MAC USERS!

Bioconda has broken the latest build of MEGAHIT for macOS. Please follow the instructions below, either Using micromamba or Using conda, to install Captus and AFTER Captus is installed please run the following two commands to get a functional MEGAHIT (if you used conda just replace micromamba by conda):

micromamba activate captus
micromamba install -c bioconda megahit=1.2.9=hfbae3c0_0

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Tip

USE BUSCO DATABASES AS REFERENCE TARGETS

Now Captus can parse any BUSCO lineage database and use it as reference targets. 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 --captus_assemblies_dir my_assemblies --nuc_refs ~/Downloads/aves_odb10.2021-02-19.tar.gz

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INSTALLATION

Using micromamba

The fastest way to install Captus is to create an isolated software environment using micromamba (https://mamba.readthedocs.io/en/latest/installation.html), if you don't have micromamba it can very easily be installed: For linux with bash shell:

curl micro.mamba.pm/install.sh | bash

For macOS with zsh shell:

curl micro.mamba.pm/install.sh | zsh

. Once you have micromamba installed in your system you need to configure your channels:

micromamba config prepend channels bioconda
micromamba config prepend channels conda-forge
micromamba config list

The last command should show your current channels, the order matters:

channels:
  - conda-forge
  - bioconda
show_banner: false

Now we are ready to create a separate environment for Captus:

micromamba create -n captus captus

Finally, test that Captus was correctly installed:

micromamba activate captus
captus_assembly

Using conda

A more "mainstream" but slower way to install Captus is to create an isolated software environment using conda, if you don't have conda we recommend to install miniconda from https://docs.conda.io/en/latest/miniconda.html. Once you have conda installed in your system you need to configure your channels:

conda config --prepend channels bioconda
conda config --prepend channels conda-forge
conda config --show channels

The last command should show your current channels, the order matters:

channels:
  - conda-forge
  - bioconda
  - defaults

Now we are ready to create a separate environment for Captus:

conda create -n captus captus

conda sometimes takes too long to find and configure dependencies, if that happens we recommend installing mamba first, and installing Captus with it:

conda install mamba
mamba create -n captus captus

Finally, test that Captus was correctly installed:

conda activate captus
captus_assembly

And if the program was correctly installed you will see the main help page of Captus:

usage: captus_assembly command [options]

Captus 1.0.0: 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: 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 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

ERROR: Missing command

USAGE

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

CITATION

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