Enhanced Pipeline ‘MetaGaAP-Py’ for the Analysis of Quasispecies and Non-Model Microbial Populations using Ultra-Deep ‘Meta-barcode’ Sequencing

Christopher Noune; Caroline Hauxwell

doi:10.1101/171520

Abstract:

A pipeline developed to establish sequence identity and estimate abundance of non-model organisms (such as viral quasispecies) using customized ultra-deep sequence ‘meta-barcodes’ has been modified to improve performance by re-development in the Python programming language. Redundant packages were removed and new features added. RAM and storage usage have been optimized to facilitate the computational speeds though coding optimizations and improved cross-platform compatibility. However, computational limits restrict the approach to barcodes spanning a maximum of 30 polymorphisms. The modified pipeline, MetaGaAP-Py, is available for download here: https://github.com/CNoune/IMG_pipelines

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