SECAPR

SECAPR processes raw sequencing reads from sequence capture (target/hybrid enrichment) and Massive Parallel Sequencing (MPS) platforms into multiple sequence alignments for phylogenetic and phylogeographic analyses.

Key Features:

• Targeted sequence capture processing: Designed to process sequence capture (target/hybrid enrichment) datasets commonly generated from non-model organisms.
• Raw reads to alignments: Transforms raw sequencing reads into multiple sequence alignments suitable for downstream phylogenetic analyses.
• Quality control and plotting: Implements quality-control steps and plotting functions to assess data quality and inform parameter selection.
• Parallel processing: Supports simultaneous processing of multiple samples to increase throughput on large datasets.
• Reproducible workflow: Provides an automated workflow aimed at reproducible handling and analysis of large-scale sequencing datasets.
• Empirical demonstration: Applied to sequence capture data from the palm genus Geonoma (Arecaceae) as an empirical example.

Scientific Applications:

• Phylogenetic inference: Produces multiple sequence alignments for use in phylogenetic tree reconstruction and related evolutionary analyses.
• Phylogeography and population studies: Enables generation of aligned loci for phylogeographic and population-level investigations using sequence capture data.

Methodology:

Automates the transformation of raw sequencing reads into aligned sequences, incorporates quality-control steps, and supports parallel processing of multiple samples for sequence capture/MPS datasets.