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Rauf Salamzade edited this page Aug 2, 2022 · 1 revision

TBD

Wiki pages Pages 23

Home
00. Background & Considerations
01. Installation
02. The Object Oriented Core of lsaBGC
03. Quick Start & In Depth Tutorial: Exploring BGCs in Cutibacterium
04. Generating Required Inputs for lsaBGC
05. Clustering BGCs into GCFs
06. Refinement of BGCs Belonging to GCF
07. Visualizing GCFs Across Phylogenies
08. High throughput Detection of New GCF Instances Across Draft Genome Assemblies
09. Assessing Evolutionary Linkage of BGCs with their Genome wide Contexts
10. Population Genetics Analysis of Genes Found in a GCF
11. Discovering Novel Variations in GCF Genes from Raw Sequencing Reads
12. The lsaBGC AutoAnalyze Workflow
13. Overview of lsaBGC AutoAnalyze's Final Results
14. lsaBGC Easy Tutorial
15. Benchmarking Gene Detection through Expansion vs. DiscoVary
16. Detailed Walkthrough Describing Framework Used for Salamzade et al. 2022
17. GSeeF Visualizing GCF Cluster Presence and Annotation Along a Species Phylogeny
18. Measuring codon usage dissimilarity of BGCs to their background genomes
19. Plot Sample BGC ome
20. Matching GCFs to Reference BGCs in MIBiG
X. Additional Programs and Scripts

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