mbtools
is a collection of helpers that we use to analyze microbiome data. It makes it easier to run some common analyses and is pretty opinionated towards our own experiences.
mbtools
sees analyses as a workflow consisting of several analysis steps and final outputs based on those. This is pretty similar to Qiime 2 and most of the functionality in mbtools
is supposed to be orthogonal and not in competition to those other excellent tools.
mbtools
mostly works on the following data types:
For mbtools
a workflow step is based on input data and a configuration, thus having the function signature step(object, config)
. Most steps can be chained with the pipe operator to yield workflows. For instance, the following is a possible workflow with mbtools
:
library(mbtools)
config <- list(
demultiplex = config_demultiplex(barcodes = c("ACGTA", "AGCTT")),
preprocess = config_preprocess(truncLen = 200),
denoise = config_denoise()
)
output <- find_read_files("raw") %>%
demultiplex(config$demultiplex) %>%
quality_control() %>%
preprocess(config$preprocess) %>%
denoise(config$denoise)
This clearly logs the used workflow and the configuration. The configuration can also be saved and read in many formats, for instance yaml.
config.yaml:
preprocess:
threads: yes
out_dir: preprocessed
trimLeft: 10.0
truncLen: 200.0
maxEE: 2.0
denoise:
threads: yes
nbases: 2.5e+08
pool: no
bootstrap_confidence: 0.5
taxa_db: https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1
species_db: https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1
hash: yes
This can now be reused by someone else: