pmpcosta / bimico

Example Microbiome Core methods

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Short tutorial for BiMiCo package basic functions

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The BiMiCo (Biomap Microbiome Core-tools) package offers single-step preprocessing of 16S microbial marker gene sequencing raw data files for 454 and Illumina platforms.
The current tutorial and example data is aimed at the simple preprocessing of 454-generated fastq data. For more options and details, please see the "BiMiCo_tutorial_LONG" document. (pls contact me for appropriate demo dataset)

Install dependencies

• Install CRAN dependencies

install.packages("BiocManager")
install.packages("ggplot2")

• Install Bioconductor dependencies

BiocManager::install("Biobase")
BiocManager::install("Biostrings")
BiocManager::install("phyloseq")
BiocManager::install("dada2")

Load required packages

library(BiMiCo)
library(ggplot2) \

Specify INPUTS:

• fastq files (directory containing raw fastq files intended for analysis exclusively, no other files):

rawfqs <- "./Demo_data/raw_fqs"

• sample phenodata (sample names in rows, sample variables in columns):

phedat <- read.csv("./Demo_data/phenodata_demo.csv", row.names=1)

• if not already contained in sample phenodata, please specify PRIMER TYPE (amplified region):

phedat$primer_type <- "V3-V4"

• taxonomy database to use with DADA2 (default is Greengenes v.13.5):

txset <- "./Demo_data/gg_13_8_train_set_97.fa.gz"

Specify OUTPUT folders:

• directory to write quality-filtered fastq files to:

filtered_fqs <- "./Demo_data/filt_fqs"

• directory to write various outputs(ASV table, figures & graphs) to:

out_main <- "./Demo_data/results/"

Generate a summary report based on the desired variable column of phenodata (case/control, sample source, sequencing batch...)

• UNDER DEVELOPMENT: specify phyloseq object, variable of interest, output file basename- PDF of ordination and top 4 ASVs, extended in the future

bimico_summary(toy_set, "clinical_group", "ex1")