genomics-assembly

De novo genome assembly reconstructs contigs directly from short or long reads. This Skill automates the process using assemblers like SPAdes, Megahit, Flye, and Canu, generating contigs and reporting quality metrics.

Yes, you can assemble a bacterial genome using long reads with Flye. The Skill wraps Flye and other assemblers to automate de novo genome assembly and then evaluates assembly quality and completeness.

Genome assembly quality assessment uses metrics like N50, N90, L50, L90, GC content, and contig length distribution. This Skill calculates these metrics comprehensively, remaining compatible with QUAST standards.

Yes, this genome assembly Skill supports short reads by wrapping SPAdes and Megahit. It standardizes the process of generating contigs from short reads while providing comprehensive quality assessment metrics.

The best way to assess assembly completeness is by evaluating N50, N90, and GC content. This Skill automatically calculates these essential metrics and contig length distributions immediately after generating the assembly.

De novo genome assembly requires memory-intensive processes because it reconstructs large genomes from fragmented reads without a reference. This Skill automates these complex computations using assemblers like Canu and Flye.