Example Jovian report
Data shown below is based on public data, available on ENA via accession ID PRJNA491626. It contains Illumina paired-end data of faeces from Cameroonian patients with the aims of identifying viral gastroenteritis aetiological agents. We have no affiliation to the owners of this dataset.
By clicking here or the button below an interactive Jovian report demo will start. Please note, we are using the free Binder service to show you this demo report. Since it's a free service it will take a couple of minutes to start. Furthermore, we had to reduce the data-footprint below 10 MB. So some parts are downsized or omitted due to technical constraints. A local Jovian installation will be fully functional.
The Quality Control metrics report is an aggregate report of various bioinformatics tools. In the case of Jovian, several statistical sets are shown:
- General statistics of the input samples
- Number of reads with a given insert size for every sample, done with
Picard - Number of reads that were aligned with a given reference (default: Human Genome), done with
Bowtie2 - Number of trimmed reads, done with
Trimmomatic - Additional Quality Control statistics provided by
FastQC
Open an example report in a separate tab by clicking here or see the screenshot below (click here for a larger version).
The Read-based composition barchart gives you a quick overview of the contents of each sample processed by Jovian.
Low-quality reads are those that did not meet the stringency settings as specified in the config file.
Unclassified reads are those that could not be assigned to a taxa.
Remaining reads are those that could not be assembled into contigs longer than the user specified minimum contig length.
Open an example barchart in a separate tab by clicking here or see the screenshot below (click here for a larger version)
Krona charts give detailed and interactive pie-chart to investigate the contents of your (metagenomic) samples.
Open an example Krona pie-chart in a separate tab by clicking here or see the screenshot below (click here for a larger version)
Heatmaps are stratified into Superkingdoms, (non-phage) viruses, phages and bacteria. They aggregate the taxonomic classifications of all samples and are particularly useful for larger datasets. When hovering over the heatmaps additional information about that taxa is shown.
Open an interactive example in a separate tab by clicking here or see the screenshot below (click here for a larger version)
Please note, many viruses have no "order" taxonomic rank so always check the "family" taxonomic rank.
Open an interactive example in a separate tab by clicking here or see the screenshot below (click here for a larger version)
Please note, many viruses have no "order" taxonomic rank so always check the "family" taxonomic rank.
Open an interactive example in a separate tab by clicking here or see the screenshot below (click here for a larger version)
Open an interactive example in a separate tab by clicking here or see the screenshot below (click here for a larger version)
A filterable, spreadsheet-like, table showing the taxonomically classified scaffolds in the processed (metagenomic) samples. These scaffolds are annotated with additional metrics/metadata and are listed per-sample and per-scaffold.
As example, see the screenshot below (click here for a larger version)
A filterable, spreadsheet-like, table showing the scaffolds that could not be taxonomically classified. These scaffolds are annotated with additional metrics/metadata and are listed per-sample and per-scaffold.
As example, see the screenshot below (click here for a larger version)
Shown below are the predicted hosts for viruses found in the processed (metagenomic) samples, (click here for a larger version).
The taxonomic classifications shown above are limited to the species level. For several virus families and genera we have typing-tools that facilitate sub-species level taxonomic labeling, AKA "typing". These are shown below. The virus typing outputs are currently not automatically generated via Jovian due to overloading and crashing the web-service. Virus-typing can be optionally performed after a Jovian analysis, however, we kindly ask you to use this sparingly as to not overload and break the web-service.
Click here for a bigger version of the screenshot below.
Click here for a bigger version of the screenshot below.
Click here for a bigger version of the screenshot below.
Click here for a bigger version of the screenshot below.
This IGVjs based viewer allows inspection of SNPs/minority variants (quasispecies), predicted ORFs, depth of coverage and GC contents for each sample and each scaffold interactively and in great detail.
Click here for a bigger version of the screenshot below.
Click here for a bigger version of the screenshot below.
A filterable, spreadsheet-like, table listing all minority variants / SNP's identified in the processed (metagenomic) samples.
Click here for a bigger version of the screenshot below.
Software logs, database timestamps, runtime statistics and pipeline settings of the current run are presented to the user.
Open an example Snakemake_report in a separate tab by clicking here, and see the screenshots below.
Click here for a bigger version of the screenshot below.
Click here for a bigger version of the screenshot below.
Binder was used for hosting the demo report and htmlpreview for rendering the HTML files.