Captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

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

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 -c bioconda 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 -c bioconda 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 0.9.90: 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/

SethMusker / Captus