Web-based SymTyper¶
Brief Overview¶
To run SymTyper from the web, follow these instructions:
First, invoke symtyper main submission page (http://www.symtyper.com). You should be presented with the following page in SymTyper’s Main Screen.
SymTyper’s Main Screen
To submit a new analysis, browse and select your input fasta file and a valid ids file (Fasta Input Format) and then click submit (See New SymTyper Analysis Screen).
New SymTyper Analysis Screen
The next screen will provide you with the URL where the output can be accessed. Depending on the input size, the processing can take between few minutes to hours (See Processing Screen and Job URL). Please copy the URL for future access. Job will be hosted on the SymTyper site for 15 days.
Processing Screen and Job URL
If the anlysis completed successfully, you will be presented with the a summary table where the various componenents of the analysis can be accessed (SymTyper Results Main Screen). The results are gouped by section: Clades, Subtypes, Multiples, Trees, Breakdown. These sections are explained below.
SymTyper Results Main Screen
| Section | Description |
|---|---|
| Clades | Shows the breakdown of clades per sample. The results can be viewed or download as a matrix or show as a piechart per sample |
| Subtypes | Shows the breakdowns of subtypes per sample. The results can be viewed independently for the Perfect, Unique and ShortNew subtypes |
| Multiples | The graphs shows the distribution of sequences for each clade contaning multiple hits. The definition of a Multiple hits is described in the Multiples section |
| Trees | Describes the breakdown of the number of sequences assigned to the internal nodes, and the clades per sample. The tree representation show the combined count for all the samples |
| Breakdown | Shows a Sunburst representation of the Clades and subtypes by sample |
Clades View¶
The Clades View shows a table view of the distribution of HITS, NOHITS, LOW and AMBIGUOUS hits per sample. Clicking the View Chart provides access to the clades distribution for each sample. The complete results and disbtribution of clades per sample can be downloaded from the results main page (see Pie Chart Distribution of Clade per Sample).
Pie Chart Distribution of Clade per Sample
Subtypes View¶
The Subtypes Views shows the breakdown of subtypes per sample. The results can be viewed independently for the Perfect, Unique and the ShortNew subtypes. The subtypes are assigned based on the blast results of the query sequences to the clade specific references (See Subtypes Distribution per Clade).
Subtypes Distribution per Clade
| Section | Description |
|---|---|
| Perfect | A query sequence that aligns perfectly or with very high similarity to a unique symbiont reference in the database (e.g., 100% similarity to 100% of the length of the target) |
| Unique | A query sequence that aligns unambiguously to symbiont reference in the database. (e.g., \(>=\) user defined % similarity to 100% target length and the bit score for the best hit is at least 3 orders or magnitude larger than than that for the second hit); |
| ShortNew | A query sequence shorter than the average sequence in the reference database but aligns with high similarity to a unique reference according to the dynamic similarity threshold (See Dynamic Similarity) |
Multiples View¶
The Multiples View is a graphical representation of the corrected subtypes count to which ambiguous sequences map. The algortihm used to resolved multiple hits is described in the Ambiguous Hit Correction and detailed in the manuscript (See Subtypes Distribution for the Corrected Ambiguous Hits).
Subtypes Distribution for the Corrected Ambiguous Hits
The breakedown of subtypes for Resolved under the “Resolved tab”
Trees View¶
For each clade phylogeny, this view compiles the number of times a Lowest Common Ancestor was identified for an ambiguous sequence (after the Ambiguous Hit Correction stage). The tree can be downloaded in the Newick NHX format and viewed or parsed in phylogeny applications (See Newick NHX Format). A matrix file comparing results across samples can be be found in output archive available for download from the main page.
Breakdown View¶
Using user-friendly graphical Sunburst representation, this view summarizes the intricate structure of Symbiodinium clades and subtypes in a single or multi-sample view. Highlighting a level of the Sunburst charts display its structure and the percentage of sample reads assigned to it (See Subtype Breakdown Vizualization).
Subtype Breakdown Vizualization