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Rauf Salamzade edited this page Aug 1, 2024 · 25 revisions

Welcome to the lsaBGC-Pan wiki!

lsaBGC-Pan puts together some programs from the original suite (e.g. lsaBGC-Cluster, lsaBGC-See, lsaBGC-ComprehenSeeIve, and GSeeF) and some new programs (e.g. zol, lsaBGC-Reconcile [an updated version of lsaBGC-Divergence], and lsaBGC-Sociate). lsaBGC-Pan works on both bacterial and fungal genomes and can jointly process both antiSMASH and GECCO BGC predictions.

In summary, lsaBGC-Pan is a newer and recommended workflow to the previously available lsaBGC-Easy.py and lsaBGC-EukEasy.py workflows. We plan to continue development of this workflow but maintain support for lsaBGC-Easy.py and lsaBGC-EukEasy.py.

Contents

  • [1] overview of lsaBGC-Pan
  • [2] comparison to lsaBGC-Easy.py and lsaBGC-EukEasy.py
  • [3] installation guide
  • [4] tutorial on GECCO based analysis of BGCs from Cutibacterium avidum and Cutibacterium acnes
  • [5] tutorial on joint AntiSMASH & GECCO analysis of BGCs from Streptomyces olivaceus
  • [6] tutorial on AntiSMASH analysis of BGCs from Aspergillus flavus
  • [7] explanation of final spreadsheet and visual reports
  • [8] overview of lsaBGC-Reconcile and lsaBGC-Sociate
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