refseq_masher: What’s in your sequence data?

refseq_masher searches your sequence data against a Mash database of 54,925 NCBI RefSeq Genomes to find what NCBI RefSeq genomes match or are contained within your sequence data.

This tutorial will run refseq_masher against a publicly available reads set.

Get tutorial reads data

Let’s get the WGS data for SRR1203042 from EBI:

Illumina MiSeq paired end sequencing; Whole genome shotgun sequencing of Salmonella enterica subsp. enterica serovar Abony str. FNW19H84 by Illumina MiSeq

Download forward and reverse reads for SRR1203042:

Initial Data

It is assumed the sequence files (forward and reverse) SRR1203042_1.fastq.gz and SRR1203042_2.fastq.gz have been uploaded into a sample as described in the Web Upload Tutorial. Before starting this tutorial you should have a project with a sample as seen below:

refseq-masher-samples

Add Sample to Cart

Select sample “SRR1203042” and add it to your Cart:

add-to-cart

Once the samples have been added to the cart, the samples can be reviewed by clicking on the Cart button at the top.

cart-button

Select refseq_masher Pipeline

Once inside the cart all available pipelines will be listed in the main area of the page.

pipeline-select

Configure and Launch refseq_masher Analysis

refseq-pipeline-page

Modify the parameters to run refseq_masher if desired:

refseq-pipeline-customize

Click the “Launch Pipeline” button to submit the analysis.

launch-button

Once the pipeline is selected, the next page provides an overview of all the input files, as well as the option to modify parameters.

It will take a while for the RefSeqMasher analysis pipeline to complete. Along the top of the page you can check the current step of the analysis and at the bottom of the Details tab you can select if you would like to receive an email upon pipeline completion or error. The email option is only available if the analysis is not in COMPLETED or ERROR state.

analysis-in-progress

When the Ref Seq Masheranalysis has completed, you will be able to view the results of the analysis. Note that not all files have an available preview and as such are not displayed in the Output File Preview but are downloaded when selecting the Download All Files button.

refseq-results

You should see 2 files under “Output File Preview”:

To download individual files select the next to the Download All Files and select the file to download.

refseq-download-individual-files

To download al the files generated by the analysis, please select the Download All Files button.

refseq-download-all-files

Viewing and Interpreting the Results

Matches - SRR1203042-refseq-masher-matches.tsv

Below is the top result from SRR1203042-refseq-masher-matches.tsv transposed for readability:

Field Value
sample SRR1203042
top_taxonomy_name Salmonella enterica subsp. enterica serovar Abony str. 0014
distance 0.00650877
pvalue 0
matching 328/400
full_taxonomy Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Abony; str. 0014
taxonomic_subspecies Salmonella enterica subsp. enterica
taxonomic_species Salmonella enterica
taxonomic_genus Salmonella
taxonomic_family Enterobacteriaceae
taxonomic_order Enterobacterales
taxonomic_class Gammaproteobacteria
taxonomic_phylum Proteobacteria
taxonomic_superkingdom Bacteria
subspecies enterica
serovar Abony
plasmid  
bioproject PRJNA224116
biosample SAMN01823751
taxid 1029983
assembly_accession GCF_000487615.2
match_id ./rcn/refseq-NZ-1029983-PRJNA224116-SAMN01823751-GCF_000487615.2-.-Salmonella_enterica_subsp._enterica_serovar_Abony_str._0014.fna

Given that our sample, SRR1203042, was from an Illumina MiSeq sequencing run of strain Salmonella enterica subsp. enterica serovar Abony str. FNW19H84, the top refseq_masher result confirms that the WGS is Salmonella enterica subsp. enterica serovar Abony.

For more info on interpreting refseq_masher matches results, see refseq_masher matches documentation

Contains - SRR1203042-refseq-masher-contains.tsv

If a read set potentially has multiple genomes, it can be “screened” against the database to estimate how well each genome is contained in the read set.

Below are the first 5 rows and columns of SRR1203042-refseq-masher-contains.tsv:

sample top_taxonomy_name identity shared_hashes median_multiplicity
SRR1203042 Salmonella enterica subsp. enterica serovar Typhimurium 0.99953 397/400 36
SRR1203042 Salmonella enterica subsp. enterica serovar Typhimurium 0.997614 385/400 285
SRR1203042 Salmonella enterica subsp. enterica serovar Typhimurium 0.997614 385/400 285
SRR1203042 Salmonella enterica subsp. enterica serovar Choleraesuis 0.997614 385/400 284
SRR1203042 Salmonella enterica subsp. enterica serovar Choleraesuis 0.997614 385/400 284

We can see that SRR1203042 mostly contains k-mers belonging to Salmonella enterica subsp. enterica NCBI RefSeq Genomes.

About some of the fields in SRR1203042-refseq-masher-contains.tsv:

For more info on interpreting refseq_masher contains results, see refseq_masher contains documentation and the Mash Screen documentation.

Viewing Provenance Information

To view the pipeline provenance information, please select the Provenance tab.

refseq-provenance

The provenance is displayed on a per file basis. Clicking on refseq-masher-matches.tsv file will display it’s provenance. Expanding each tool will display the parameters that the tool was executed with.

refseq-provenance-tools

Viewing Pipeline Details

To view analysis details, please select the Settings tab. From here you can view the analysis name, analysis description, analysis id, pipeline and pipeline version used by the analysis, analysis priority, when the analysis was created, and duration of the analysis.

refseq-settings

To edit an analysis name, please select the Pencil icon next to the analysis name. Once you have edited the analysis name, pressing the ENTER key on your keyboard or clicking anywhere outside of the text box will update the name. To cancel editing a name you can either hit the ESC key on your keyboard or if the name has not been changed you can also click anywhere outside of the text box.

refseq-settings-edit-name

To view samples used by the analysis, please select the Samples tab.

refseq-settings-samples

To share analysis results with other projects, please select the Manage Results tab.

refseq-settings-share

To delete an analysis, please select the Delete Analysis tab.

refseq-settings-delete