Update: As of September 2024 Assembler will be added at no cost when you upgrade or renew maintenance. Contact Support if you have not yet been upgraded.
To assemble various types of sequencing reads, follow these steps.
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- Choose File | New | Assembly Project to create a new empty project file.
Then follow one of the following:
To create a de novo assembly from Sanger reads
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- Click on the Add Reads tool bar button, then select the sequence files you wish to assemble and click on the Open button. Read(s) file(s) can also be drag and dropped on the open Assembly Project window.
- Click Phred to basecall sequences in the project. Note that if no sequences are selected, phred will be run on ALL of the files in the project.
- Click Phrap to assemble the reads.
To create a de novo assembly from NGS datasets
To create a de novo assembly from Nanopore or Pacbio datasets
- Click on the Add Reads tool bar button, then select the sequence files you wish to assemble and click on the Open button. File(s) can also be drag and dropped on the open Assembly Project window. Paired reads files are automatically detected.
- Double click on the reads and ensure they are correctly flagged as Pacbio reads.
- Choose Flye to assemble the reads.
To create a reference assembly
- Click the Add Reads button, then select the sequence files you wish to assemble and click on the Open button.
- Click Add Ref, select the sequence file(s) you wish to align the reads against and click on the Open button.
- Click Bowtie to map all read files against all of the reference sequences in the project.