very-dreamy-blastvdb: an easy to use wrapper for blastn_vdb and tblastn_vdb
blastn_vdb and tblastn_vdb are new BLAST implementations from NCBI that use
one or more Sequence Read Archive (SRA) accessions as nucleotide databases for
nucleotide or protein queries (respectively).
I created very-dreamy-blast as an easy to use wrapper around blast_vdb, with options provided by the user on each run, without having to change any parameters hidden in some bash script.
./run_vdb.sh -s SRX00001,[SRX00002],[...] -q QUERY_INPUT.FASTA -t nucl|prot [-e #] [-d] [-n]
Required:
-s: A comma-separated list of 1 or more SRA Accession(s) to build BLAST databases from
-q: A query file in FASTA format
-t: The type of query, 'nucl' or 'prot' (do not include the quotes)
Optional:
-e: e-value threshold for the BLAST search, in scientific notation. Default: 1e-9
-d: By default, the blastn_vdb task is megablast (for most similar hits).
If you would like to instead search for more divergent matches,
you may use the -d flag to switch the task to discontiguous-megablast
-n: Similar to the -d flag, except it switches the BLAST task to blastn,
which is optimized for somewhat similar hits.