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User Guide to SeqMan Ultra — 18.0

18.0

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User Guide to SeqMan Ultra — 18.0
- User Guide to SeqMan Ultra — 18.0

SeqMan Ultra Overview
SeqMan Ultra Tutorials
- Whole genome reference-guided workflow
- Whole genome de novo workflow with mate pair data
- Analysis of a whole genome de novo assembly
- De novo assembly using Sanger data
- RNA-Seq de novo transcriptome workflow
  - Part A: Setting up the transcriptome assembly in SeqMan NGen
  - Part B: Viewing annotated transcripts in SeqMan Ultra
- Gap closure workflow
- Reference-guided alignment of Sanger/ABI data
Getting Started
SeqMan Ultra Interface
- Welcome screen
- Views
- Panels
Assemble Sequences
- Assemble small-to-medium sets of Sanger data
  - Quality score calculations
  - End-trimming based on averaged quality scores
- Assemble multi-sample Sanger data
- Assemble NGS data or large sets of Sanger data
Open an Existing Assembly
- Navigate between open assemblies
Contigs
- Organize contigs and scaffolds
- Edit a contig
- Close a gap between contigs
- Display contig information in a graphical or tabular view
- Rename a contig
- Reassemble contigs
Features
Tracks
- Ruler track
- Contig track
- Coverage track
- Pair consistency track
- Features track
- Split reads track
- Translation track
- Trace track
- Majority track
- Sample-alignment track
- Rename a track manually
- Rename tracks automatically using specified data fields
Customize the Look and Layout
- Customize the appearance and layout of views
- Customize the layout of other window components
- Save the layout and apply it to other projects
Search Within the Project
- Search for and select a read sequence by name
- Search for elements within a contig
- Search for a numerical position on a contig
Search for Sequence Matches
- Set up local BLAST databases
- Search for sequence matches using BLAST
- Search for text or accession number matches using Entrez
  - Filter text search results
- Access ID dialog
- Save and reopen saved search results
Make a Selection
Specify, Save, and Apply Parameters
- Consensus parameters
  - Consensus calling algorithms
- Strategy Viewing and Coverage parameters
- Pair Specifier parameters
- Assembly parameters
- End Trimming parameters
- Variant Discovery parameters
Export
- Export an image of a view
- Export data to a file
- Export data from the Variants view
- Export data from the Text, Table or Pairwise views
- Export an assembly in BAM format
Save, Close and Exit
Appendix
- Set preferences
- Troubleshoot the error “A different version is running”
- IUPAC codes
- Supported file types
- Installed Lasergene file locations
- Research references

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Appendix

The Appendix contains the following topics:

Troubleshoot the error
IUPAC codes
Supported file types
Installed Lasergene file locations
Research references

Save, Close and Exit

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