Satsuma
Introduction
Synteny-focused aligner
Usage
To load the module:
module load satsuma
The main executable is
Satsuma
Help file output
Satsuma: Wrapper around high-sensitivity alignments.
Available arguments:
-q<string> : query fasta sequence -t<string> : target fasta sequence -o<string> : output directory -l<int> : minimum alignment length (def=0) -t_chunk<int> : target chunk size (def=4096) -q_chunk<int> : query chunk size (def=4096) -n<int> : number of blocks (def=1) -lsf<bool> : submit jobs to LSF (def=0) -nosubmit<bool> : do not run jobs (def=0) -nowait<bool> : do not wait for jobs (def=0) -chain_only<bool> : only chain the matches (def=0) -refine_only<bool> : only refine the matches (def=0) -min_prob<double> : minimum probability to keep match (def=0.99999) -proteins<bool> : align in protein space (def=0) -cutoff<double> : signal cutoff (def=1.8) -same_only<bool> : only align sequences that have the same name. (def=0) -self<bool> : ignore self-matches. (def=0)
