mmseqs2 is a modern and robust aligner. This PR adds capability to add MMSeqS2 to superfocus, and releases the databases too.
There are multiple problems using diamond in a cluster environment (and, for example, with snakemake). mmseqs2 should solve many of those problems.
There is one gotcha - the program is called mmseqs2 but the binary is mmseqs so I try to accept either on the cli, and then use mmseqs2 in the directory names (to be clear) and mmseqs as the executable name.
mmseqs2 is a modern and robust aligner. This PR adds capability to add MMSeqS2 to superfocus, and releases the databases too.
There are multiple problems using
diamondin a cluster environment (and, for example, with snakemake). mmseqs2 should solve many of those problems.There is one gotcha - the program is called
mmseqs2but the binary ismmseqsso I try to accept either on the cli, and then usemmseqs2in the directory names (to be clear) andmmseqsas the executable name.