Captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

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Installation

The simplest way to install Captus is to first create an isolated software environment with the dependencies with miniconda:

conda create -n captus -c bioconda -c conda-forge "clipkit>=1.3.0" "python>=3.6" pandas plotly tqdm perl-bioperl-core=1.007002 bbmap falco fastqc mafft mmseqs2 megahit pigz vsearch

Then clone the Captus repository:

git clone https://github.com/edgardomortiz/Captus

Now install Captus within the conda environment you created:

conda activate captus
cd Captus
pip install .

Run the following command:

captus_assembly

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

usage: captus_assembly command [options]

Captus 0.0.17: 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: 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

Alternatively, you can skip the installation with pip and simply run the following command in your conda environment (you will need to add Captus' directory to your $PATH to make it available from anywhere in the computer):

captus_assembly-runner.py