This repository contains code for downloading and processing shotgun metagenomics data from the National Ecological Observatory Network (NEON). This accompanies a tutorial for processing the raw reads, accessible on F1000 Research.
Two BLAST analyses are described in the tutorial: one focuses on N-cycling genes, and the other on antibiotic resistance genes. There is an example script here for parsing the BLAST output (in Python) and writing it to a CSV file, blast_parser.py. Then, the scripts beginning with normalize_gene_counts can be used to normalize data using the DeSeq R package and visualize the results in R.
To update metadata_metagenome.csv (the file with raw NEON sample read counts - necessary for normalization), run this code in R (takes < 3 minutes):
library(neonUtilities)
library(dplyr)
metadata <- loadByProduct(dpID = 'DP1.10107.001', check.size = FALSE, package = 'expanded')
sequence_metadata <- metadata$mms_metagenomeSequencing %>%
select(dnaSampleID, sampleTotalReadNumber, sampleFilteredReadNumber) %>%
distinct() %>% rename(sampleID = dnaSampleID)
write.csv(sequence_metadata, "./metadata_metagenome.csv")
Included in this repository, in the ARO directory, is an ontology file from CARD:
Alcock et al. "CARD 2020: antibiotic resistome surveillance with the Comprehensive Antibiotic Resistance Database" Nucleic Acids Research, 48: D517-D525. https://www.ncbi.nlm.nih.gov/pubmed/31665441
NCycDB_pathways.csv contains gene pathway data from NCycDB:
Tu, Qichao, et al. "NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes." Bioinformatics 35.6 (2019): 1040-1048.