HTML Report

Concept

No successful marker extractions can be achieved without successful assemblies. Even though this assemble module offers presets tuned for different data types, it is recommendable to repeat this step some times with different parameters to find optimal settings for your own data.

Captus assists you in this tedious process by automatically generating a useful report for assembly evaluation.
Just open captus-assembly_assemble.report.html with your browser (internet connection required) to get general assembly statistics across all your samples!

Tip

The entire report is based on data stored in captus-assembly_assemble.stats.tsv.
All tables and plots in the report are interactive powered by Plotly.
Visit the following sites once to take full advantage of its interactivity:
- https://plotly.com/chart-studio-help/getting-to-know-the-plotly-modebar
- https://plotly.com/chart-studio-help/zoom-pan-hover-controls

1. Summary Table

This table shows the general assembly statistics for each sample.

Features:

Switch the Sort by dropdown to re-sort the table by any column value.
Cells are color-coded according to value (high = green; low = pink).

Description of each column

Column^a	Description	Unit
Sample	Sample name	-
Total Length Passed	Cumulative length of all contigs passed GC content filter	bp
Total Length Removed	Cumulative length of all contigs removed by GC content filter (shown only when `--max_contig_gc` argument is enabled)	bp
Number of Contigs Passed	Number of contigs passed GC content filter	-
Number of Contigs Removed	Number of contigs removed by GC content filter (shown only when `--max_contig_gc` argument is enabled)	-
*Mean Length	Mean contig length	bp
*Contig N50	Weighted average of contig lengths that 50% of total assembly length consists of contigs over this length	bp
*Longest Contig	Longest contig length	bp
*Shortest Contig	Shortest contig length	bp
*≥1 kbp Contigs	Percentage of contigs over 1 kbp in total number of contigs	%
GC Content Passed	Mean GC content of contigs passed GC content filter	%
GC Content Removed	Mean GC content of contigs removed by GC content filter (shown only when `--max_contig_gc` argument is enabled)	%
*Mean Depth	Mean contig depth	x

2. Visual Stats

This plot shows the statistics shown in the table above in addition to more detailed statistics as a bar graph.

Features:

Switch the dropdown at the y-axis to switch the variable to show.
Click on the legend to toggle hide/show of each data series.

Description of each variable

Variable^a	Description	Unit
Total Length	Cumulative length of all contigs	bp
Number of Contigs	Number of contigs	-
Mean Length	Mean contig length	bp
*Median Length	Median contig length	bp
*Contig N50	Weighted average of contig lengths that 50% of total assembly length consists of contigs over this length	bp
*Longest Contig	Longest contig length	bp
*Shortest Contig	Shortest contig length	bp
*Contig Breakdown by Length	Percentage of contigs over 1, 2, 5, and 10 kbp in total number of contigs	%
*Length Breakdown by Contig Length	Percentage of contigs over 1, 2, 5, and 10 kbp in total length of contigs	%
GC Content	Mean GC content of contigs	%
*Mean Depth	Mean contig depth	x
*Contig Breakdown by Depth	Percentage of contigs with over 1, 2, 5, and 10 x depth in total number of contigs	%

Created by Gentaro Shigita (11.08.2021)
Last modified by Gentaro Shigita (17.10.2022)

HTML Report

Concept

Contents

1. Summary Table

2. Visual Stats