Cluster refinement

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Cluster refinement

“refinement.sh” (calling “remove_orfs.sh”)

  • input:
    • Cluster db “data/mmseqs_clustering/marine_hmp_db_03112017_clu_fa”
    • Cluster info table “data/mmseqs_clustering/marine_hmp_db_03112017_clu_info.tsv.gz
    • Cluster with spurious and/or shadows ORFs “data/spurious_and_shadows/marine_hmp_info_shadow_spurious.tsv.gz”
    • Set of good cluster from the validation “data/cluster_validation/good_cl.tsv”
  • output:
    • FFINDEX database of refined clusters in “data/cluster_refinement/ffindex_files/”
    • Tab separated file containing the refined cluster ids and their ORFs in “data/cluster_refinement/”

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