> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/pathogenwatch/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/genome-assembly/short-read-assembly.md).

# Short Read Assembly

We also provide a small-scale assembly service, primarily for the benefit of smaller labs or individual researchers without bioinformatics resources. Please be aware resources are limited, and provided under our [fair usage policy](#fair-usage-policy).

The assembly pipeline is based on [Shovill version 1.1.0-2022Dec](https://github.com/tseemann/shovill). Please ensure you cite it if you use the results in a publication.

{% hint style="info" %}
You need to be logged in to use the assembly service.
{% endhint %}

## Usage

1. Start by visiting the upload page: <https://pathogen.watch/upload>.
2. Drag pairs of FASTQ files (can be more than one pair at a time) onto the page and they will start being uploaded.
3. You will start to see progress as your genomes are assembled and analysed.

{% hint style="info" %}
FASTQ files must be uploaded in pairs. Most standard FASTQ naming conventions are supported:

* Sample-A\_1.fastq.gz / Sample-A\_2.fastq.gz
* Sample-A\_R1.fastq.gz / Sample-A\_R2.fastq.gz
* Sample-A\_R1.fq.gz / Sample-A\_R2.fq.gz
* Sample-A.1.fq.gz / Sample-A.2.fq.gz
* Sample-A\_R1\_001.fastq.gz / Sample-A\_R2\_001.fastq.gz
  {% endhint %}

An initial quality check on the FASTQ is carried out to check the file format and minimum nucleotide coverage. When your genomes have finished being assembled you can view the results as normal.

After assembly, the genome's summary metrics are compared against [QualiBact](/pathogenwatch/technical-descriptions-of-analysis-tools/assembly-qc.md), a framework of community-agreed, species-specific quality thresholds. Once the species is known, QualiBact supplies expected ranges for a panel of assembly statistics — genome size, GC content, N50, number of contigs, longest contig, and total coding sequences. Thresholds currently cover 300+ bacterial species and are derived automatically by the qualibact-engine from large public reference collections (e.g. RefSeq), with manual curation where the automated fit is poor; they are published as guidance, not biological absolutes.

## Expected results

Assembling and analysing one genome can take 15-120 minutes, depending on coverage, genome size and the spare compute capacity.

## Constraints

We only support Illumina paired-end read data (or equivalent) in `.fastq.gz` format. We welcome feedback on other sequencing platforms and suitable assembly pipelines.

The maximum FASTQ filesize is 900MB per file.

#### Species

As a Spades-based pipeline, we expect to receive bacterial, viral or haploid fungal genomes. SPAdes is not designed to handle diploid assemblies, and any results would be unreliable.

## Fair Usage Policy

{% hint style="warning" %}
We have set a limit of **50 assemblies** **per month** per user.
{% endhint %}

The Pathogenwatch assembly service is provided for free to the community with support from our funders. Assemblies are expensive to generate, requiring us to constrain the number of genomes run, and we expect all users to be considerate of this fact. If we identify individuals or organisations attempting to abuse the facility we will delete their account(s) from Pathogenwatch.

We would like to also note that over the last 5 years, no one has abused the assembly service. We would love it to stay this way!

### Download the Docker images to run locally

The original SPAdes image: `staphb/shovill:1.1.0-2022Dec@sha256:2e074e095e5886d432f6f05b7c4bf23dde3b467e8cfeef6f831c347fac197a1a`

The Pathogenwatch STDIN -> STDOUT image (`siso`): `pathogenwatch/siso:assembly-2`

## How to cite

**The SPAdes assembler:** Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes De Novo Assembler. *Curr Protoc Bioinformatics*. 2020;70(1):e102. doi:10.1002/cpbi.102

**Shovill:** Seemann T (2016) *Shovill* Github <https://github.com/tseemann/shovill>