Plugins

Categories - Jump to: Breakdown | Export | Analysis | Third party | Miscellaneous

Breakdown

Breakdown plugins - Jump to: Field Breakdown | Two Field Breakdown | Unique Combinations | Polymorphisms | Publication Breakdown | Sequence Bin Breakdown

Field Breakdown

Summary: Breakdown of query results by field

The field breakdown plugin displays the frequency of each value for fields, alleles and schemes. Output is in the form of dynamic charts, maps, and tables. Data can be exported as an Excel file, SVG image, or FASTA file.

Documentation bigsdb.readthedocs.io

Launch 'Field Breakdown'

Two Field Breakdown

Summary: Breakdown of one field against another

The two field breakdown plugin generates a table breaking down the frequencies of one field against another. This is analagous to a spreadsheet pivot table. Any primary metadata field, locus, or scheme field can be used and the output can be exported as an Excel spreadsheet.

Documentation bigsdb.readthedocs.io

Launch 'Two Field Breakdown'

Unique Combinations

Summary: Determine frequencies of unique field combinations

The Unique Combinations plugin calculates the frequencies of unique file combinations within an isolate dataset. Primary metadata fields, allele designations and scheme fields can be combined. Results are returned in an Excel spreadsheet.

Documentation bigsdb.readthedocs.io

Launch 'Unique Combinations'

Polymorphisms

Summary: Tool for analysing polymorphic sites for particular locus in an isolate dataset

This plugin generates a schematic of the selected locus showing all the polymorphic sites present in the selected dataset. These are also shown in a tabular form with precise frequencies for each nucleotide at every position.

Documentation bigsdb.readthedocs.io

Launch 'Polymorphisms'

Publication Breakdown

Summary: Breakdown of query results by publication

This plugin shows all publications linked to isolates in a query dataset or within the whole database. The results can be filtered by author or year. The output includes full citation details and a link to display all isolates linked to any listed publication.

Documentation bigsdb.readthedocs.io

Launch 'Publication Breakdown'

Sequence Bin Breakdown

Summary: Breakdown of sequence bin contig properties

The sequence bin breakdown plugin calculates statistics based on the number and length of contigs in the sequence bin as well as the number of loci tagged for each isolate record. Using this latter metric against a cgMLST scheme can be a good indicator of genome quality. Values for number of contigs, total sequence length, mean contig length and contig length distribution are charted.

Documentation bigsdb.readthedocs.io

Launch 'Sequence Bin Breakdown'

Export

Export plugins - Jump to: Export | Contig export | Sequence Export

Export

Summary: Export dataset generated from query results

The Export plugin creates a download file of any primary metadata, secondary metadata, allele designations, scheme designations, or publications for isolates within a selected dataset or for the whole database. The output file is in Excel format.

Documentation bigsdb.readthedocs.io

Launch 'Export'

Contig export

Summary: Analyse and export contigs selected from query results

This plugin enables the contigs associated with each isolate in a dataset to be downloaded in FASTA format. They can also be downloaded in batch mode as a TAR file. The contigs included in the download can be filtered based on the percentage of the sequence that has been tagged with a locus so that poorly annotated regions can be analysed specifically.

Documentation bigsdb.readthedocs.io

Launch 'Contig export'

Sequence Export

Summary: Export concatenated allele sequences in XMFA and FASTA formats

This plugin creates concatenated XMFA and FASTA files of selected loci for a particular dataset. These sequences can optionally be aligned, using either MAFFT or MUSCLE, facilitating quick analysis of the outputs in third-party phylogenetic analysis packages.

Documentation bigsdb.readthedocs.io

Launch 'Sequence Export'

Analysis

Analysis plugins - Jump to: Codon Usage | Gene Presence | Genome Comparator | BLAST | rMLST species identity | PCR

Codon Usage

Summary: Determine codon usage for specified loci for an isolate database query

The codon usage plugin calculates the absolute and relative synonymous codon usage by isolate and by locus for any dataset or the whole database. Specific loci or the loci that are members of a particular scheme can be chosen for analysis.

Documentation bigsdb.readthedocs.io

Launch 'Codon Usage'

Gene Presence

Summary: Analyse presence/absence of loci for dataset generated from query results

The Gene Presence analysis tool will determine whether loci are present or absent, incomplete, have alleles designated, or sequence regions tagged for selected isolates and loci. If a genome is present and a locus designation not set in the database, then the presence and completion status are determined by scanning the genomes. The results can be displayed as interactive pivot tables or a heatmap. The analysis is limited to 500,000 data points (locus x isolates).

Documentation bigsdb.readthedocs.io

Launch 'Gene Presence'

Genome Comparator

Summary: Compare genomes at defined loci or against loci defined in a reference genome

Genome Comparator is used to compare whole genome data of isolates within the database using either the database defined loci or the coding sequences of an annotated genome as the comparator. Output is equivalent to a whole genome MLST profile, a distance matrix calculated based on allelic differences and a NeighborNet graph generated from this distance matrix. The analysis facilitates the determination of precisely which loci vary among isolates. Additionally, user-uploaded genomes that are not contained in the database can be analysed alongside genomes that are.

Documentation bigsdb.readthedocs.io

Launch 'Genome Comparator'

BLAST

Summary: BLAST a query sequence against selected isolate data

The BLAST plugin enables you to BLAST a sequence against any of the genomes in the database, displaying a table of matches which can be downloaded in Excel format. In addition, the matched sequence regions are made available for download in FASTA format, either with or without surrounding flanking sequence.

Documentation bigsdb.readthedocs.io

Launch 'BLAST'

rMLST species identity

Summary: Use rMLST to identify species from bacterial genome assemblies

The species identification tool extracts ribosomal MLST alleles from genomes and determines the species based on the count of alleles that are uniquely found within a single species (or higher taxonomic rank if alleles unique to a species are not found). This is done by making a query via the PubMLST RESTful API to the rMLST typing database.

Documentation bigsdb.readthedocs.io

Launch 'rMLST species identity'

PCR

Summary: In silico PCR tool for designing and testing primers

The in silico PCR tool can be used to simulate PCR reactions run against genomes stored in the database. This is useful for designing and testing primers. The plugin uses the exonerate ipcress program to perform its simulation. Primers can contain wobble bases and the number of allowed mismatches for each primer can be set independently. The output is a table of predicted products, showing the number of products and their positions within a contig. It is also possible to export the predicted product sequence.

Documentation bigsdb.readthedocs.io

Launch 'PCR'

Third party

Third party plugins - Jump to: GrapeTree | iTOL | PhyloViz | Microreact

GrapeTree

Summary: Visualization of genomic relationships

GrapeTree is a tool for generating and visualising minimum spanning trees (Zhou at al. 2018 Genome Res 28:1395-1404). It has been developed to handle large datasets (in the region of 1000s of genomes) and works with 1000s of loci as used in cgMLST. It uses an improved minimum spanning algorithm that is better able to handle missing data than alternative algorithms and is able to produce publication quality outputs. Datasets can include metadata which allows nodes in the resultant tree to be coloured interactively.

Documentation bigsdb.readthedocs.io

Launch 'GrapeTree'

iTOL

Summary: Phylogenetic trees with data overlays

The ITOL plugin allows you to generate and visualise phylogenetic trees calculated from concatenated sequence alignments of selected loci (or the loci belonging to a particular scheme). Currently, only Neighbour-joining trees are supported. Datasets can include metadata which allows nodes in the resultant tree to be coloured. Datasets are uploaded to the Interactive Tree of Life website (Letunic & Bork 2016 Nucleic Acids Res 44(W1):W242-5) for visualisation.

Documentation bigsdb.readthedocs.io

Launch 'iTOL'

PhyloViz

Summary: Creates phylogenetic inference and data visualization for sequence-based typing methods

PhyloViz Online is a tool for generating and visualising minimum-spanning trees based on allelic profiles. This plugin generates datasets that are then uploaded to PhyloViz Online for visualisation. Datasets can include metadata which allows nodes in the resultant tree to be coloured interactively.

Documentation bigsdb.readthedocs.io

Launch 'PhyloViz'

Microreact

Summary: Open data visualization and sharing for genomic epidemiology

Microreact is a tool for visualising genomic epidemiology and phylogeography (Argimón et al 2016 Microb Genom 2:e000093). Individual nodes on a displayed tree are linked to nodes on a geographical map and/or timeline, making any spatial and temporal relationships between isolates apparent. The Microreact plugin generates Neighbour-joining trees from concatenated sequences for any selection of loci or schemes and uploads these, together with country and year field values, to the Microreact website for display.

Documentation bigsdb.readthedocs.io

Launch 'Microreact'

Miscellaneous

Database Fields

Summary: Display description of fields defined for the current database

This plugin fully describes primary and secondary metadata fields defined in the database. The data type (integer, float, text, or date), lists of allowed values or ranges, whether the field is compulsory or optional and the maximum length of values is displayed.

Launch 'Database Fields'