Genewiz_16S: Genewiz_16S

In baynec2/biolabr: Useful functions for the biologist

Genewiz_16S

Description

This function is designed to be a consise method to determine the taxonomy of several samples that have been sent for 16S sanger sequnecing.

Usage

Genewiz_16S(
  folder_path,
 
    blast_db_path = file.path("/Volumes/kaleidobio/Shared/D2/Departments/Research/Biology/biolabr/16SMicrobial/16SMicrobial"),
 
    accessionToTaxa_path = file.path("/Volumes/kaleidobio/Shared/D2/Departments/Research/Biology/biolabr/accessionTaxa.sql"),
  similarity = 99
)

Arguments

folder_path	This is the path to the folder containing the forward and reverse 16S reads.
blast_db_path	This is the path to the 16SMicrobial database
accessionToTaxa_path	This is the path to the accessionTaxa.sql database.
similarity	This is the similarity cutoff to consider (entered as a percentage). If multiple taxa are reported to have the given level of similarity, the most granular level of taxonomy where there is consensus will be returned.

Details

The function does this by generating consensus sequences from a folder containing several forward and reverse 16S sanger sequencing reads and then BLASTs them against the NCBI database. This folder containing the foward and reverse reads is intended to be obtained through Genewiz 16S although it doesn't necessarily have to have been for the function to work. The files must have the following naming conventions:

In the folder containing all of the data, the forward read for any given sample name should be followed by SeqF.ab1. ex "Sample1SeqF.ab1"

The reverse read for the same sample should be the same sample name followed by SeqR.ab1. ex "Sample1SeqR.ab1"

This function is designed to handle any number of paired forward and reverse samples in the initial input folder.

This function also depends on the user having installed blast on their computer. This can be done by going to ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ The user will then have to download the 16SMicrobial database. This can be downloaded at ftp://ftp.ncbi.nlm.nih.gov/blast/db/v4/

Once blastn is downloaded the user will then need to provide a database that converts the NCBI acession number to the actual taxonomy. This can be done by using the prepareDatabase('accessionTaxa.sql') function that is part of the taxonomizer package (https://github.com/sherrillmix/taxonomizr). Note that it is best to store the acessionTaxa database somewhere central because it is quite large (~60 GB).

Value

a dataframe containing the taxonomy assignments corresponding with the samples in the folder path.

Examples

taxa = Genewiz_16S("Folder_with_Genewiz_Results",
blast_db_path = "where_I_store_the_16SMicrobial_database",
accessionToTaxa_path = "where_I_store the acessionTaxa.sql_file_I_got_by_using_taxonomizer_package"
similarity = 99)

baynec2/biolabr documentation built on Aug. 8, 2022, 12:02 a.m.