How do I create an Assembly Project

To assemble a set of sequences follow these steps. Look at Assembling Sequences for more details about each of these steps.

Chose 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

Click on the Add Reads tool bar button, then select the sequence files you wish to assemble and click on the Open button. Note that you can hold down the <shift> key to select multiple sequences to import. Read(s) file(s) can also be drag and dropped on the open Assembly Project window.
Choose Analyze | Base Call (phred) to run the phred algorithm on all of the sequences in the project. Note that if no sequences are selected, phred will be run on ALL of the files in the project.
(Optional) Chose Analyze | Vector Trim (cross_match) to mask vector sequences in the reads. You will need to import the vector sequences you used in the vectors tab of the cross_match dialog. The files must be in either MacVector or FastA format.
Choose Analyze | Assemble (phrap) to assemble all of the sequences of the project.

To create a de novo assembly from NGS datasets

Click on the Add Reads tool bar button, then select the sequence files you wish to assemble and click on the Open button. Note that you can hold down the <shift> key to select multiple sequences to import. Read(s) file(s) can also be drag and dropped on the open Assembly Project window. Paired reads files are automatically detected and flagged correctly.
Choose either SPAdes or Velvet to assemble all of the sequences of the project.

To create a de novo assembly from PacBio or Nanopore datasets

Click on the Add Reads tool bar button, then select the sequence files you wish to assemble and click on the Open button. Note that you can hold down the <shift> key to select multiple sequences to import. Read(s) file(s) can also be drag and dropped on the open Assembly Project window. Paired reads files are automatically detected and flagged correctly.
Choose Flye to assemble all of the sequences of the project.

To create a reference assembly

Click on the Add Reads tool bar button, then select the sequence files you wish to assemble and click on the Open button. Note that you can hold down the <shift> key to select multiple sequences to import. Read(s) file(s) can also be drag and dropped on the open Assembly Project window.
Click on the Add Ref tool bar button, then select the sequence file(s) you wish to align the reads against and click on the Open button. Reference sequences cannot be added by drag and drop.
Choose Analyze | Bowtie to run the Bowtie algorithm on all of the sequences in the project. Note that if no sequences are selected, Bowtie will be run on ALL of the files in the project. However, if any sequences are selected then the reference sequence and at least one reads file must be selected.

After assembling

Double-click on a contig to open it in the Contig Editor.

You can not only edit sequences in the contig editor but you can also directly run any MacVector nucleic acid analysis function on the contig consensus sequence.

Finally you can save the consensus sequence in MacVector format by choosing File | Save As.. from the contig editor window. You can also save the assembly project itself at any time and you will be prompted to save any changes when you close the project window.