SeqMan NGen’s project setup wizard lets you upload files and optimize parameters for your assembly. After choosing your desired workflow in the first (“Workflow”) screen, subsequent wizard screens will vary according to the workflow chosen. Most workflows include 5-8 wizard screens. Each screen is described in a separate topic:
- Welcome screen (appears only when you first open SeqMan NGen)
- Workflow (used in all workflows)
- Analysis Options
- Assembly Log
- Assembly Options
- Assembly Output (used in all workflows)
- Assembly Summary
- Cloud Monitor
- Define Binding Proteins
- Input Assemblies
- Input Assembly
- Input Contig Sequences
- Input Host Files
- Input Reference (Sequence, Genome, for Scaffolding, etc.)
- Input Sequences (including Long Read, Short Read)
- Input VCF Files
- Input Viral Genomes
- Post Assembly Options
- Preassembly Options
- Run Assembly Project
- Set Contaminant
- Set Up Experiments
- Set Up Replicate Sets
- Polishing Options
- Transcript Annotation Database
- Options tabs
Additional information pertaining to the wizard can be found in Add and remove files in the wizard and Use editing commands in the wizard.
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