mlstverse is a general purpose identification software. Currently database for Mycobacterium species (consists of MTB complex and nontuberculous mycobacteria) is available.
> git clone https://github.com/ymatsumoto/mlstverse
> git clone https://github.com/ymatsumoto/mlstverse.Mycobacterium.db
> R
>>> if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
>>> BiocManager::install("Rsamtools", version = "3.8")
>>> install.packages("devtools")
>>> devtools::install("mlstverse")
>>> devtools::install("mlstverse.Mycobacterium.db")
Downloads Loci.fasta to your local strage. Loci.fasta is also included in mlstverse repository.
Before identifying isolates using R scripts, prepare bam files. Mapping shotgun sequence reads should be mapped to Loci.fasta using any mapping software and indexed.
> bwa mem Loci.fasta input.fastq | samtools sort - -o out.bam
> samtools index out.bam
library(mlstverse)
library(mlstverse.Mycobacterium.db)
filenames <- c("out.bam")
result <- mlstverse(filenames, threads=16)
print(result$score)| option | default | description |
|---|---|---|
| filenames | (required) Character, locations of input bam files | |
| mlstdb | mlstverse.Mycobacterium.db | (optional) MLST database |
| min_depth | 0 | (optional) Numeric, only use genes larger than the minimum reads depth |
| min_ratio | 0.1 | (optional) Numeric, only use genes larger than the ratio to maximum reads depth |
| th.pvalue | 0.05 | (optional) Numeric, filter by threshold value in Kolmogorov–Smirnov test |
| th.score | 0.1 | (optional) Numeric, filter by threshold value in MLST score |
| threads | 1 | (optional) Numeric, number of threads |
| normalize | TRUE | (optional) Boolean, if TRUE, normalize coverage |
| samfile | NULL | (optional) BamFile object in RSamtools package, input bam file. Excluive with filenames option. |
| method | "default" | (optional) Character, scoring methods. "default" and "sensitive" are available. |
MLST database used in the mlstverse is compatible with other MLST methodologies. We are currently preparing to be also available pubmlst database from mlstverse.
Not published yet.
Released under MIT + file LICENCE.
If you find some problem, please contact [email protected]