MMseqs2
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mmseqs easy-search faster?
Hello, I'm using the following command to find the closest references for multiple reads. As both the database and the fasta file are quite big, it takes quite some time. I tried using max-seqs=7, however, the output is really not good giving results that have only 91% while there are more sequences at 96%? Does someone have an idea how to optimize this command while being sensitive (or is this not possible)?
Thanks!
mmseqs easy-search {FASTA_GI} {REF_DB_GI} \
--search-type 3 --start-sens 2 -s 7 --sens-steps 3 --alignment-mode 3 \
--sort-results 1 --threads {cpus_per_task} \
{TSV_GI_SEARCH}