Installation

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:

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

Important for macOS users

One of the builds of the latest version of MEGAHIT (v1.2.9) on Bioconda is broken. To ensure you install a functional one, please specify the build number as follows:

conda create -n captus -c bioconda -c conda-forge captus megahit=1.2.9=hfbae3c0_0
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 1.1.0: 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 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 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 manually install all the dependencies listed below:

Dependency Version URL
Python >=3.6 https://www.python.org
BBTools https://jgi.doe.gov/data-and-tools/bbtools
BioPerl https://bioperl.org
ClipKIT >=1.3.0 https://github.com/JLSteenwyk/ClipKIT
Falco >=0.3.0 https://github.com/smithlabcode/falco
FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc
MAFFT https://mafft.cbrc.jp/alignment/software
MEGAHIT 1.2.9 https://github.com/voutcn/megahit
MMseqs2 https://github.com/soedinglab/MMseqs2
MUSCLE >=5.1 https://www.drive5.com/muscle
pandas >=2.1.0 https://pandas.pydata.org
Plotly https://github.com/plotly/plotly.py
pigz https://zlib.net/pigz
Salmon >=1.10.0 https://github.com/COMBINE-lab/salmon
tqdm https://github.com/tqdm/tqdm
VSEARCH https://github.com/torognes/vsearch
YAML https://metacpan.org/pod/YAML

* The following two dependencies are bundled with Captus, so no additional installation is required.

Dependency Version URL
BLAT 37x1 http://hgdownload.soe.ucsc.edu/admin/exe
Scipio 1.4.1 https://www.webscipio.org

Once you have all the dependencies installed, you can proceed to clone the repository and install Captus as follows:

git clone https://github.com/edgardomortiz/Captus.git
cd Captus
pip install .
captus -h

Alternatively, you can run Captus using the wrapper script captus_assembly-runner.py as follows:

git clone https://github.com/edgardomortiz/Captus.git
./Captus/captus_assembly-runner.py -h

Created by Edgardo M. Ortiz (06.08.2021)
Last modified by Gentaro Shigita (19.12.2024)