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Title: The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis
The largest dataset of soil metagenomes has recently been released by the National Ecological Observatory Network (NEON), which performs annual shotgun sequencing of soils at 47 sites across the United States. NEON serves as a valuable educational resource, thanks to its open data and programming tutorials, but there is currently no introductory tutorial for accessing and analyzing the soil shotgun metagenomic dataset. Here, we describe methods for processing raw soil metagenome sequencing reads using a bioinformatics pipeline tailored to the high complexity and diversity of the soil microbiome. We describe the rationale, necessary resources, and implementation of steps such as cleaning raw reads, taxonomic classification, assembly into contigs or genomes, annotation of predicted genes using custom protein databases, and exporting data for downstream analysis. The workflow presented here aims to increase the accessibility of NEON’s shotgun metagenome data, which can provide important clues about soil microbial communities and their ecological roles.  more » « less
Award ID(s):
1638577
PAR ID:
10502082
Author(s) / Creator(s):
; ; ; ;
Publisher / Repository:
F1000research
Date Published:
Journal Name:
F1000Research
Volume:
10
ISSN:
2046-1402
Page Range / eLocation ID:
299
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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