Blast: Create taxonomic tables based on Blast alignment of the reads

In katrikorpela/mare: Microbiota Analysis in R Easily

Create taxonomic tables based on Blast alignment of the reads

Description

The function BLASTS the reads againts the NCBI database, selects the best hit for each read, and creates taxonomic tables based on the best hits. A blast taxonomy file is created with the following columns: read name, GI of the best hit, similarity, and evalue.

Usage

Blast(finalreads, read.table, NCBItaxonomy, folder.name = "")

Arguments

finalreads	Directory of the processed reads, a file called finalreads.fasta produced by ProcessReads.
read.table	Directory of the read table, produced by ProcessReads.
NCBItaxonomy	Directory of the NCBI taxonomy files.
folder.name	Name for the new folder where the taxonomic tables will be written. Should be the same as the folder.name given to function ProcessReads in order to analyse the correct reads.

Details

To run Blast, you need to install the BLAST+ command line application installed <ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/>, and the NCBI taxonomy files <ftp://ftp.ncbi.nih.gov/pub/taxonomy/>. You also need to install the R package CHNOSZ.

Author(s)

Katri Korpela

Examples

	## Not run: 

Blast(finalreads = "finalreads.fasta", read.table = "read_table.txt", NCBItaxonomy = "directory/to/NCBIdb/", folder.name = "")

## End(Not run)

katrikorpela/mare documentation built on July 17, 2022, 2:49 a.m.