run_blastn {rCRUX} | R Documentation |
Runs blastn with the seed amplicon input fasta as a query
run_blastn(
fasta,
db_dir,
temp = NULL,
ncbi_bin = NULL,
evalue = 1e-06,
align = 50000,
coverage = 50,
perID = 70
)
fasta |
a fasta-formatted string |
db_dir |
a path to a directory / directories containing one or more blast-formatted database. For multiple blast databases, separate them with a space and add an extra set of quotes. (e.g blast_db_path <- "/my/ncbi_nt/nt" or blast_db_path <- '"/my/ncbi_nt/nt /my/ncbi_ref_euk_rep_genomes/ref_euk_rep_genomes"') |
ncbi_bin |
is the path to blast+ tools if not in the user's path. Specify only if blastn and blastdbcmd are not in your path. The default is ncbi_bin = NULL - if not specified in path do the following: ncbi_bin = "/my/local/ncbi-blast-2.10.1+/bin/". |
evalue |
is the number of expected hits with a similar quality score found by chance. The default is evalue = 1e-6. |
align |
is the maximum number of subject hits to return per query blasted. The default is align = 50000. |
coverage |
is the minimum percent of the query length recovered in the subject hits. The default is coverage = 50. |
perID |
is the minimum percent identity of the query relative to the subject hits. The default is perID = 70. |
temp: |
a file path to write a temporary fasta to. The default is temp = NULL. |
Calls blastn with a fasta file as the query. The user can not add additional search parameters, but can modify the available parameters.
run_blastn takes a fasta file, and query them to a blast formatted database. The result is an output table with the following columns of data: accession, amplicon_length, pident, query_accession, accession_sequence_length, amplicon_start, amplicon_stop, sequence, evalue, BLAST_db_taxids.
Information about the blastn parameters can be found by accessing blastn -help and at NCBI.
a tibble representing the blastn results