Workflow Amplicon Sequencing report

Introduction

This report contains tables and plots to help interpret the results of wf-amplicon. The workflow was run in variant calling mode. The individual sections of the report summarize the outcomes of the different steps of the workflow (read filtering, mapping against the reference file containing the amplicon sequences, variant calling).

The input data contained:

At a glance

Key results for the individual samples are shown below. You can use the dropdown menu to view the results for a different sample.

Preprocessing

Some basic stats covering the raw reads and the reads remaining after the initial filtering step (based on length and mean quality) as well as after downsampling and trimming are illustrated in the table below.

The following plots show the read quality and length distributions as well as the base yield after filtering (but before downsampling / trimming) for each sample (use the dropdown menu to view the plots for the individual samples).

Summary

The two tables below (one per tab) briefly summarize the main results of mapping the reads to the provided amplicon references and subsequent variant calling. Percentages of unmapped reads are relative to the number of reads for that particular sample. Other percentages are relative to the total number of reads / bases including all samples.

The following table breaks the results down further (one sample–amplicon combination per row).

Depth of coverage

Coverage along the individual amplicon, (use the dropdown menu to view the plots for the individual amplicons).

Variants

Haploid variant calling was performed with Medaka. Variants with low depth (i.e. smaller than --min_coverage) are shown under the "Low depth" tab. The numbers in the "depth" column relate to the sequencing depth used to perform variant calling.