Proksee’s genome assembly functionality has been completely rewritten. The new Assembly Tool can assemble genomes directly from short and long sequencing reads.

The new Assembly Tool supports three types of assembly:

• Short-read assembly using SKESA, MEGAHIT, or SPAdes
• Long-read assembly using Flye
• Hybrid assembly from combined short and long reads using Unicycler

Users can upload raw FASTQ files and go directly from sequencing reads to an assembled genome and interactive Proksee map.

The tool also includes a comprehensive quality-control workflow. Reads are filtered and assessed before assembly, and the resulting assembly is evaluated using a range of post-assembly analyses. These include standard analyses of genome completeness, contamination, and taxonomy, as well as new approaches to k-mer completeness and contig binning.

Each analysis produces a detailed Assembly Report containing the results, figures, software and database versions, workflow settings, and checksums for the input files and final assembly. The report is designed to provide both an overview of assembly quality and the information needed to understand and reproduce the analysis.

Once assembly is complete, the assembled contigs are loaded directly into Proksee, where they can be annotated, analyzed, and visualized using Proksee’s existing tools.

The Assembly Tool is currently in beta. We welcome feedback as we continue to improve the workflow.