Is it appropriate for clustering of nucleotide contigs

[chen318liang]

Can this software be used for clustering of pooled assembled metagenome nucleotide contigs from several samples. The length of contigs is between 323 to 1,106,190. How to set the parameters to fit this purpose? I have try with default parameters, but there is less cluster produced.

Commands: mkdir cluster fa=combined.contig.fa mmseqs createdb ${fa} cluster/DB mmseqs cluster cluster/DB cluster/DB_clu tmp mmseqs createtsv cluster/DB cluster/DB cluster/DB_clu cluster/DB_clu.tsv mmseqs createseqfiledb cluster/DB cluster/DB_clu cluster/DB_clu_seq mmseqs result2flat cluster/DB cluster/DB cluster/DB_clu_seq cluster/DB_clu_seq.fasta

In addition, if OK, can the representative nucleotide contigs directly be used for the taxonomy assignment? will this affect the accuracy of result? Tanks very much!