Quantitative metagenomic alignment and taxonomic exact-matching
This is an automatic pipeline for analysis of amplicon sequence data including 16S, 18S and ITS. It wraps QIIME commands and complements them with additional analysis where QIIME is not good at, such as combine multiple sequencing runs, OTU clustering and chimeric removal with UP ARSE, alignment filtering with Gblock, removing Chloroplast sequen…
Code associated with the following manuscript, currently in review: M.S. Fischer, N.J. Patel, P.J. De Lorimier, M.F. Traxler "Prescribed fire selects for a pyrophilous soil subcommunity in a northern California mixed conifer forest"
Mineral dust is a critical source of nutrient elements for peatlands, especially nutrient-poor bogs. However, the potential for mineral dust to influence soil microbial activities remains unclear. We used flow-through peat mesocosms and simulated dust deposition. Both 16S and ITS amplicon sequencing was performed to track community structure shifts
AU microbiome molecular exploratory analyses for NSW
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