v0.4.1-415-g32ba67b900
2023_11_03_v2 (code v.2023_11_03_v2, DBs 2023_11_03_v2)
2.3
mash sketch -S 42 -k 21 -s 1000{individually} -o {query_msh_noext} {query_fa} && mash dist {plasmids_msh} {query_msh} -v {max_pvalue} -d {max_dist} > {output}
mash screen {plasmids_msh} {query_fa} -v {max_pvalue} -i {min_ident}{winner_takes_all} > {output}
blastn: 2.14.1+; Package: blast 2.14.1, build Aug 1 2023 12:22:01
tblastn: 2.14.1+; Package: blast 2.14.1, build Aug 1 2023 12:22:01
blastn -query {query_fa} -task blastn -db {plasmids_db} -out {output} -evalue 1 -perc_identity {min_ident} -qcov_hsp_perc {min_cov} -outfmt '6 qseqid sseqid qstart qend sstart send evalue bitscore pident qcovs qcovhsp'
tblastn -query {query_fa} -task tblastn -db {plasmids_db} -out {output} -evalue 1 -qcov_hsp_perc {min_cov} -outfmt '6 qseqid sseqid qstart qend sstart send evalue bitscore pident qcovs qcovhsp'
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