Genome assembly refers to the process of taking a large number of short DNA reads and putting them back together to create a representation of the whole genome from which the DNA originates. De novo genome assemblies assume no prior knowledge of the source DNA sequence length, layout or composition (i.e. no reference genome is available). The goal of an assembler is to produce long contiguous pieces of sequences (contigs) from DNA-seq reads. The contigs are then joined together to form scaffolds where possible. Short-insert paired reads provide increased information for maximizing sequencing coverage, while long-insert mate paired-end reads can pair sequence fragments across greater distances. This is especially helpful to cover highly repetitive regions.

This functionality can be found under Genome Analysis → DNA-Seq De novo Assembly.

Three assembly strategies are available:

• ABySS: ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. It implements algorithms that employ a Bloom filter, a probabilistic data structure, to represent a de Bruijn graph. ABySS is capable of assembling large genomes.

• SPAdes: SPAdes (St Petersburg genome assembler) is an assembly toolkit containing various assembly pipelines based on the Bruijn Graph. SPAdes works with Illumina and IonTorrent data and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. SPAdes is designed for small genomes, and allows to assemble single-cell MDA data as well as standard isolates.

• Flye: Flye is a de novo assembler for single-molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. Flye uses the repeat graph as a core data structure.