Kia ora and welcome the the Conservation, Systematics and Evolution Research Team repository! Here, we have a brief introduction to the command line interface (CLI), data carpentry, data management, and bioinformatic tools commonly used in this group.
This information is freely available for everyone and modifyable by members of ConSERT as bioinformatic approaches/practices inevitably change overtime. We're also open to and welcome feedback on how this documentation can be improved. 🔥
It is important to note that the information provided in this repository is simply to provide brief introduction to concepts and practices you'll likely used by members of our group. It is NOT intended to serve as the only resource you would want to access. In addition, this material has been designed to serve as a 'refresher', or reviewed as a group/alongside a more experienced lab member. As a general rule, this material can be seen as a starting point for your own learning. Therefore we aim to point folks in the general direction of useful and informative external resources that will cover this material thoroughly and in more detail than outlined here. Links to these suggested resources for additional learning will be made available within the Wiki. 😃
Below is a overview of each of the directories in this repository. To get started on any particular topic, head to the relevant directory above or click on the links provided below.
If you're working with genotyping-by-sequence data (GBS), here we provide some template scripts for running the STACKS pipeline. We outline steps for pre-processing and trimming your reads, and the next steps for either genome alignment or an alignment free approach to SNP discovery.
If you're working with Illumina resequence data and are in posession of a reference genome, here we provide template scripts for quality control of reads, read alignment and quality metrics.
Outline some simple tips and tricks for assessing ONT basecalling, read quality and trimming.
Here outline suggested methods for estimating heterozygosity, admixture, ROH, rarefaction, XXX?