blastn: Seach with Blastn.

In iferres/quickMLST: Quick Multi Locus Sequence Typing Analisys

Description

Seach nucleotide sequences in a nucleotide database.

Usage

blastn(genome = "", db = "", outdir = ".", n_threads = 1L, eval = 1e-06)

Arguments

genome	The query. A nucleotide fasta file.
db	The subject. A nucleotide blast database as created by makeblastdb.
outdir	Where to put the blast output file.
n_threads	integer. The nomber of cores to use.
eval	Evalue reporting threshold.

Value

The path to the blastn output. The blastn output is written in the following format as specified by -outfmt option in Blast+ program:

-outfmt '6 qseqid sseqid pident gaps length slen evalue qseq'.

Author(s)

Ignacio Ferres

References

Altschul, Gish, Miller, Myers & Lipman. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.

iferres/quickMLST documentation built on Dec. 22, 2020, 5:10 p.m.