I have a fairly large BLAST output from a metagenomics project with millions of lines per sample. The input sequences for the blast search were prodigal annotated proteins. I have been looking for a while now to find a suitable program that calculates the LCA of the BLAST outputs of the sequences.
I have looked into the following softwares:
MEGAN6: This is based on a UI (there is a command line interface, which is only available for certain editions). I am very hesitant to ever use any GUI, so this is not optimal.
BASTA: In principle, this tool would be suitable. However, the implementation is not ideal, since it doesn't allow for parallel processing of files (it locks the database folder) and it is incredibly slow when running it on larger files.
What alternatives are out there? I am debating whether it's worth writing everything from scratch, but usually it isn't.
Any inputs would be highly appreciated.