README.md

blast+ container

Main tools:

• blast+

This is meant to assist in local blast searches. No blast databases will be maintained in this container. Be sure to mount your relevant Volumes with --volumes or -v when using the command line.

blast+ is actually a suite of tools. blast+ v.2.15.0 includes:

$ ls /ncbi-blast-2.15.0+/bin/
blast_formatter
blast_formatter_vdb
blast_vdb_cmd
blastdb_aliastool
blastdbcheck
blastdbcmd
blastn
blastn_vdb
blastp
blastx
cleanup-blastdb-volumes.py
convert2blastmask
deltablast
dustmasker
get_species_taxids.sh
legacy_blast.pl
makeblastdb
makembindex
makeprofiledb
psiblast
rpsblast
rpstblastn
segmasker
tblastn
tblastn_vdb
tblastx
update_blastdb.pl
windowmasker

Currently not supported, but could be:

get_species_taxids.sh # requires E-direct
update_blastdb.pl     # requires perl

Example Usage

# making a blast database
makeblastdb -dbtype nucl -in fasta.fa

# query
tblastn -query query.fasta -db fasta.fa -outfmt '6' -out blast_hits.txt

More documentation can be found at https://www.ncbi.nlm.nih.gov/books/NBK569856/ and https://www.ncbi.nlm.nih.gov/books/NBK279690/