Assexon: Assembling Exon Using Gene Capture Data

Area of Science:

• Bioinformatics
• Genomics
• Evolutionary Biology

Background:

• Exon capture is widely used for phylogenomic studies in non-model organisms.
• Reference-based assembly methods are unsuitable for species with wide phylogenetic divergence.
• Existing de novo assembly methods struggle with low read depth, large files, and paralogs.

Purpose of the Study:

• To develop a streamlined pipeline, Assexon, for de novo assembly of targeted exons and flanking sequences from raw sequencing reads.
• To evaluate Assexon's performance against established pipelines like PHYLUCE and HybPiper.

Main Methods:

• Assexon pipeline for de novo assembly of targeted exons.
• Testing with exon capture data from *Lepisosteus osseus* and *Boleophthalmus pectinirostris*.
• Comparative analysis with PHYLUCE, HybPiper, and a custom pipeline (CP).

Main Results:

• Assexon assembled significantly more loci than PHYLUCE and HybPiper.
• Assexon demonstrated superior speed, running at least twice as fast as PHYLUCE and HybPiper, and seven times faster than CP.
• Assexon and CP successfully avoided paralogs, unlike PHYLUCE and HybPiper.

Conclusions:

• Assexon is an accurate and efficient tool for assembling large exon capture datasets.
• The pipeline includes features for filtering, statistical analysis, and selecting reliable phylogenetic loci.
• Assexon offers a robust solution for phylogenomic studies requiring multi-locus data from non-model organisms.