Welcome to the Solu Platform, the simplest way to analyze bacterial and fungal WGS samples. This guide describes our methodology, helping you to accurately cite and publish your results.

Table of contents

Using the platform

Using the platform is as simple as it gets. Just drag-and-drop your FASTQ or FASTA files in and click “Start upload”. That’s it! The analyses start automatically and finish in 2 to 10 minutes.

Solu also offers a sequencing service, where we take care of both sequencing and analysis.

Analysis pipeline

The platform runs a variety of genomic characterization and phylogenetic analyses, designed to cover the majority of research and epidemiological use cases. It builds on top of best practice open source tools, supplemented by some in-house tooling.

The platform supports isolate WGS samples for bacteria and fungi.

Architecture plan - t (1).jpg

1. Supported input formats

The pipeline supports paired-end FASTQ reads or assembled FASTA files as input formats. FASTQ uploads are recommended for best result accuracy. Compressed gzip archives (.gz) are supported for both filetypes.

2. De novo assembly

Raw reads are quality checked using FastQC v0.12. and quality corrected with fastp v0.23.4. The pre-processed reads from fastp are assembled using Shovill v1.1.0.

3. Assembly QA and standardization

Assembly quality is assessed with Quast v5.2.0, and expected genome size is checked for the most common organisms using NCBI genome API. Assembly format is standardized using any2fasta v0.4.2.

4. Species identification