Pangu LIMS Docs

Genome Puzzle Master Manual

GPM Workflow

• Upload Subject and Reference Genomes.
• Run preliminary alignments of each subject Genome to the Reference.
• Run an assembly of each Genome.
• “Clean Up” each Chromosome for the assemblies.
• Fill any possible gaps using alternative assemblies of the same subject.
• Eliminate any identifiable contamination.

GPM Basic User Guide

• GPM Main Interface
• Uploading A New Genome
• Running Preliminary Alignments
• Creating a Project and Assigning Genomes
• Creating an Assembly
• Running an Assembly
• Chromosome View
• “Cleaning Up” and Moving Contigs
• Contig View
• Gap Filling and Merging Contigs
• Breaking Contigs
• Flipping Contigs
• Alignment Checker
• Unplaced Contigs
• Troubleshooting

GPM assemblyRun

• AssemblyRun operations

• Screenshot of assemblyRun interface

Visualization of typical available data in GPM

• GPM assemblyCtg view of a 500-KB region

AssemblySeqs, top and bottom, are shown as overlapping (yellow) and fully redundant assemblySeqs are gray. The retained (green) and removed (gray) portions of assemblySeqs are indicated.

• Chromosome-scale view of a 500-KB region that compares two genome assemblies to a Reference sequence

The Reference Sequence is shown in the middle (bright green) with alignments (yellow) to each assemblyCtg (violet) at the top and bottom. The assemblyCtg order can be changed by drag-and-drop.

Flowchart for processing unitigs with postHGAP