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.