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Assembly Workflow

Assembly

The assembly workflow uses assembly-based approaches to give higher-confidence gene identity assignment than raw read assignment alone.

The assembly step determines the proper order of the reads, and assembles the genome. The assembly tool may use short reads (~350 or fewer reads), or it may use long reads (>1000 reads).

Reads are assembled in order into contigs (chunks of contiguous reads). The contigs are themselves assembled into scaffolds that consist of several contigs.

The SPAdes tool can handle short or long reads, while the megahit tool works better for short reads.

Metaquast gives assembly statistics that can help evaluate the assembly (how long, number of fragments, number of contigs, number of scaffolds, etc.).

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