Usage

In order to run kakapo you will need to prepare a project configuration file and a search strategies file. The search strategies file is only required at the later stages of the pipeline. If you want kakapo to only process raw reads — to download SRA records, run Rcorrector, Trimmomatic, and to perform filtering steps — the search strategies file is not required.

The configuration files are formatted using the standard INI syntax. If you save these files with .ini extension, many popular text editors (e.g. Sublime Text, Visual Studio Code) will apply syntax highlighting which will make the editing of these files easier.

1. The Project Configuration File [structure | example] contains parameters specific to one analysis: whether or not to run certain parts of the analysis, a list of SRA accessions, paths to FASTQ files, etc.

2. The [Search Strategies File] [structure | example] contains one or more "search strategy" entries for the genes you want kakapo to search for. Each search strategy entry is intended to encapsulate the information about a gene or a gene family, which kakapo can then use to find matching RNA-Seq reads and assemble transcripts of interest in a targeted manner. Search strategy files contain no project-specific information and, once prepared, can be reused in future projects.