rbm.rb
Finds the reciprocal best matches between two sets of sequences.
See source code, Artistic license 2.0.
§ References
Camacho et al, 2009, BMC Bioinf (BLAST+); Altschul et al, 2000, JMB (BLAST); Buchfink B, Xie C, Huson D, 2015, Nat Meth (Diamond); Kent, 2002, Genome Res (BLAT); Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.
§ Requirements
§ Usage
rbm.rb --seq1 in_file --seq2 in_file --out out_file [opts]
§ Arguments
- Sequence 1*
--seq1 in_file
FastA file containing the genome 1.- Sequence 2*
--seq2 in_file
FastA file containing the genome 2.- Output*
--out out_file
Reciprocal Best Matches in BLAST tabular format. Supports compression with .gz extension.- Nucleotides
--nucl
Sequences are assumed to be nucleotides (proteins by default).- Length
--len integer
Minimum alignment length (in residues).- Fraction
--fract float
Minimum alignment length (as a fraction of the query). If set, requires BLAST+ or Diamond (see Program).- Identity
--id float
Minimum alignment identity (in %).- Bit score
--score float
Minimum alignment score (in bits).- Executables
--bin in_dir
Directory containing the binaries of the search program.- Program
--program select
Search program to be used. Default: blast+.Make sure that you have installed the search program you want to use. If you have downloaded the program, but it's not installed, please use the Executables option above.- Threads
--threads integer
Number of parallel threads to be used.- Quiet
--quiet
Run quietly (no STDERR output).