README.md

CaptureAl

Bioinformatic pipeline streamlining analysis of target enrichment sequencing data.

How to Cite

Please cite the following paper when using CaptureAl in published work:

• Crameri S., Fior S., Zoller S. & Widmer A. (2022) A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae). Molecular Ecology Resources 22(8):3087–3105.

Before you start

1. Download/Clone the CaptureAl repository
2. Follow the installation instructions.
3. Determine how to implement parallel computing in your computing environment (GNU parallel or bsub)

Get started

Once the installation is complete, follow the tutorial step by step. You can also skip preprocessing of reads and jump-start to CaptureAl STEP 1 (parallel or bsub) if your reads are already quality-trimmed.

Post-process Workflows for

• Phylogenetics
• Population Genetics

Pipeline overview

The pipeline is divided into seven steps, shown below. For each step, there is a limited number of scripts that have to be executed, and these scripts often execute other scripts located in the repository. Parts of these graph are also in the tutorial pages.

Pipeline authors

Simon Crameri & Stefan Zoller