HCK and ABAA: A Newly Designed Pipeline to Improve Fungi Metabarcoding Analysis.

ABSTRACT:

Introduction

The fungi ITS sequence length dissimilarity, non-specific amplicons, including chimaera formed during Polymerase Chain Reaction (PCR), added to sequencing errors, create bias during similarity clustering and abundance estimation in the downstream analysis. To overcome these challenges, we present a novel approach, Hierarchical Clustering with Kraken (HCK), to classify ITS1 amplicons and Abundance-Base Alternative Approach (ABAA) pipeline to detect and filter non-specific amplicons in fungi metabarcoding sequencing datasets.

Materials and methods

We compared the performances of both pipelines against QIIME, KRAKEN, and DADA2 using publicly available fungi ITS mock community datasets and using BLASTn as a reference. We calculated the Precision, Recall, F-score usi

SUBMITTER: Mlaga KD 

PROVIDER: S-EPMC8134036 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature