notes: diamond hits scripts, mmseqs2 script (cdhit alternative)

notes/mmseqs2.sh

+# https://github.com/soedinglab/MMseqs2/wiki#batch-sequence-searching-using-mmseqs-search
+# https://github.com/soedinglab/MMseqs2/wiki#set-sensitivity--s-parameter
+# https://github.com/soedinglab/MMseqs2/wiki#how-to-find-the-best-hit-the-fastest-way
+
+conda activate /home/users/vgalata/miniconda3/envs/ONT_pilot/pipeline/c363035f
+
+# data
+asm1="/mnt/lscratch/users/vgalata/ont_pilot/results/annotation/prodigal/lr/flye/proteins.faa"
+asm2="/mnt/lscratch/users/vgalata/ont_pilot/results/annotation/prodigal/sr/metaspades/proteins.faa"
+db1="lr_flye"
+db2="sr_metaspades"
+out12="${db1}__${db2}"
+out21="${db2}__${db1}"
+
+# db
+mmseqs createdb ${asm1} ${db1}
+mmseqs createdb ${asm2} ${db2}
+
+# index
+mmseqs createindex ${db1} tmp
+mmseqs createindex ${db2} tmp
+
+# search
+mmseqs search ${db1} ${db2} ${out12} tmp --start-sens 1 --sens-steps 3 -s 7 --threads 5 -v 3
+mmseqs search ${db2} ${db1} ${out21} tmp --start-sens 1 --sens-steps 3 -s 7 --threads 5 -v 3
+
+# tables
+mmseqs convertalis ${db1} ${db2} ${out12} ${out12}.tsv --format-output "query,target,qcov,tcov,evalue,pident,nident,gapopen,mismatch,alnlen,qstart,qend,qlen,tstart,tend,tlen"
+mmseqs convertalis ${db2} ${db1} ${out21} ${out21}.tsv --format-output "query,target,qcov,tcov,evalue,pident,nident,gapopen,mismatch,alnlen,qstart,qend,qlen,tstart,tend,tlen"