SPAdes (St Petersburg genome assembler) is a de novo assembler intended for sequencing reads from many different sources. It has been designed to handle Illumina and IonTorrent reads. However, it will also do hybrid assemblies with PacBio and Oxford Nanopore and Sanger reads.
One of the shortcomings of the popular Illumina Next Generation Sequencing platform is that, even when using paired-end reads, the short read lengths make it difficult to resolve long repeats and generate full length genomic sequences. Even "simple" bacterial genomes generally have multiple Insertion Sequence elements of a few kb in length scattered around the chromosome. The result is that most assembly contigs end in repeat sequences and can only be ordered and assembled into complete genomes with great difficulty. So called "long reads", such as those produced by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), potentially solve this problem as individual reads can be many kb in length, thus spanning entire repeat sequences and reading into unique genomic sequence on each side. Unfortunately, at present, both long read technologies are highly error prone resulting in assemblies which may be long, but are of very low quality. One solution is to use hybrid assemblies, with a mixture of short reads to provide high quality sequence data, and long reads to provide a scaffold to resolve repeat sequences. MacVector with Assembler includes the SPAdes assembler which can automatically perform these hybrid assemblies.
By default, when you Add Reads in .fastq format to a MacVector assembly project, MacVector assumes the reads are from an Illumina platform. However, it does automatically detect paired end reads. Here is a project populated with a pair of Illumina files and a single Oxford Nanopore minION file.
Note how the minION file appears in the Status column as "Illumina Unpaired". This status needs to be changed so that SPAdes knows what type of data it represents. You can double-click on the Status column item to bring up a dialog allowing you to set the data type.
Once the Status is set appropriately, SPAdes will automatically perform a hybrid assembly on the reads. In many cases, this will result in significantly longer contigs, often the full length of small bacterial genomes, while still maintaining the high quality consensus sequence from the Illumina paired-end reads.