To activate captus

conda activate captus

Generally, renaming samples is to think on how we want the names in the final phylogenetic tree. But if names are too long or subject to change, we can use codes that later can be replaced by names, but this requires some programming skills.

Special characters that are safe to use in the sample name are dash (-) and underscore (_) (underscore is commonly used to replace spaces in many phylogenetic programs).

Do not use spaces or other special characters (e.g. ! " # $ % & ( ) * + , . / : ; < = > ? @ ] [ \ ^ { | } ~).

Also, do not use double underscore (__) as captus uses them internally.

The format that is used in this pipeline:

Genus_speciesDNA#_R1.fastq.gz
Genus_speciesDNA#_R2.fastq.gz

Within home directory, create a folder captus_work then set this folder as current directory

mkdir captus_work
cd captus_work

Create folder 00_raw and put the raw reads (FASTQ files) into this folder.

mkdir 00_raw

then run captus clean

captus clean -r 00_raw

Using the command above (without specifying the output folder), captus will produce the clean reads automatically in folder 01_cllean_reads.

Run the following command to perform de novo assembly for all the samples with default settings optimized for targeted-capture and genome skimming data.

captus assemble -r 01_clean_reads

Using the command above (without specifying the output folder), captus will produce the assemblies automatically in folder 02_assemblies.

A reference target file in fasta format is needed before extracting the target. In this study, the target file is baitset_clean_fixed.fasta. The file contain multiple references specified for a baitset. Formatting is important so captus can interpret the file correctly.

When multiple reference sequences per locus are found in the reference dataset, CAPTUS will evaluate during the extraction which of those references matches your assembly best based on similarity and total recovered length percentage.

captus extract \
  -a 02_assemblies \
  -n baitset_clean_fixed.fasta \
  --threads 8

Now that we have extracted the sequences out of our assemblies captus will put them together in matrices and perform clipping and filtering. Captus saves intermediate steps allowing us to access intermediate matrices. For example, we can access a locus alignment before paralogs are filtered out, so the we can use an alternative method for paralog detection.

Run the aligment:

captus align -e 03_extractions

Next step is Phylogenetic Analysis