Importing existing assemblies into an Assembly Project

Adding an existing BAM/SAM alignment to an Assembly Project

BAM/SAM files are a pair of file formats that are becoming ubiquitous for storing reference based alignments of NGS sequencing data. Along with the Fastq format for storing unaligned reads they are becoming the defacto format for NGS data.

To add a BAM/SAM file

1. Choose File | New |> Assembly Project to create a new empty Assembly Project window.
2. Click on the Add Ref tool bar button, then select the reference sequences you wish to align the imported reads against and click on the Open button.
3. Click on the Add Contig button and select your BAM/SAM file.
4. Select both files in the Assembly Project and right click on them. Select UNITE REFERENCE WITH CONSENSUS. Alternatively select UNITE REFERENCE WITH CONSENSUS AND GENERATE VCF FORMAT to generate a VCF report from that set of files at the same tim. You can also do this at a later date.

Importing Sequencher Projects

Sequencher project files (.spf) are imported into a new Assembly Project, rather than adding a new assembly object to an existing Assembly Project.

Importing Sequencher Projects

1. Choose File | Open
2. Choose a Sequencher project (.spf) file
3. A new Assembly Project will be created with the data from the Sequencher project.
4. Click FILE | SAVE AS... to save as a MacVector Assembly Project

Related Topics.

Assembler

Quick Start

Importing Fastq data

Bowtie

Bowtie Preferences

Velvet

Short Read Assembly

Base calling

Vector trimming