MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data

Area of Science:

• Bioinformatics
• Genomics
• Microbial Ecology

Background:

• Next-generation sequencing and bioinformatics are crucial for microbial population quantification using meta-barcoding.
• Existing methods face limitations due to the lack of identified barcode regions and comprehensive reference databases for many organisms.

Purpose of the Study:

• To develop a workflow and software pipeline (MetaGaAP) for identifying and quantifying genotypes in microbial populations.
• To overcome limitations of current meta-barcoding approaches by enabling custom barcode generation.

Main Methods:

• Shotgun sequencing to identify polymorphisms for custom barcode creation (under 30 polymorphisms per read).
• Amplification and sequencing of custom barcodes.
• Generation of a custom polymorphism database.
• Quantification of relative genotype abundance.

Main Results:

• The MetaGaAP pipeline was successfully validated using wild-type and tissue-culture strains of *Alphabaculovirus* (*Helicoverpa armigera* single nucleopolyhedrovirus).
• Validation confirmed accuracy by comparing amplicon and shotgun data polymorphisms and Sanger sequencing results.
• Computational constraints limit custom barcodes to a maximum of 30 polymorphisms.

Conclusions:

• MetaGaAP provides a robust method for genotype identification and quantification in microbial populations.
• This approach is particularly valuable for the ecological and pathological study of non-model organisms lacking extensive genomic resources.