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Changes from
v3.3.0
:--max_dtr_assess
. Users can enter a maximum contig length to evaluate DTRs (default 1000000). Practically, long DTR-containing contigs are probably bacterial chromosomes and should be evaluated for prophages and pruned. Since DTR-containing contigs do not get pruned, this was preventing some bacterial chromosome assemblies from getting pruning treatment. extra-long incorrect prophage calls #6hhpred_to_table.py
gene_name variable parsing, which previously incorrectly used .strip() function.MMSEQS_outdir
inget_ct3_dbs
command to avoid error.--seqtech
now effectsminimap2
settings