Introduction
This report contains tables and plots to help interpret the results of wf-amplicon. The workflow was run in de-novo consensus mode. The individual sections of the report summarize the outcomes of the different steps of the workflow (read filtering, consensus generation, re-mapping against the consensus for depth of coverage calculation).
The input data contained:
2 samples:barcode01, barcode02
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.
Reads
73
Bases
76,143
Mean length
1043.1
Mean quality
14.0
Unmapped reads
15
Consensus length
1,104
Reads
500
Bases
701,859
Mean length
1403.7
Mean quality
15.8
Unmapped reads
125
Consensus length
4,948
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.
Condition | Reads | Bases | Min read length | Max read length | Mean quality |
---|---|---|---|---|---|
Raw | 970 | 1.0 M | 48 | 3,928 | 15.5 |
Filtered | 829 | 1.0 M | 302 | 3,928 | 15.5 |
Downsampled, trimmed | 573 | 778.0 k | 358 | 3,267 | 15.6 |
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).
Quality Control
After creating a draft assembly (either with
Miniasm or with
SPOA) basic quality control is performed on the consensus candidates (i.e.
the contigs in the assembly). The QC stats for the contigs produced by the
assembly pipeline are listed in the table below. If there are no contigs for
the "miniasm" method in the table, the Miniasm step either
failed or produced contigs that were shorter than the
--force_spoa_length_threshold
parameter (and thus SPOA was run regardless of assembly quality). If
there are no contigs for "spoa", SPOA was not run as a contig produced by
Miniasm passed all filters and was selected.
Contig | Method | Length | Mean depth | Primary | Secondary | Supplementary | Primary ratio | Status | Fail reason |
---|---|---|---|---|---|---|---|---|---|
spoa_1 | spoa | 1,107 | 55.3 | 58 | 0 | 0 | 1.0 | passed | - |
Contig | Method | Length | Mean depth | Primary | Secondary | Supplementary | Primary ratio | Status | Fail reason |
---|---|---|---|---|---|---|---|---|---|
miniasm_1 | miniasm | 4,951 | 110.6 | 375 | 0 | 0 | 1.0 | passed | - |
Re-alignment summary
The table below summarizes the main results of re-mapping the reads of each barcode against the generated consensus. 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.
Sample | Reads | Unmapped | Bases | Median read length | Mean cov. | Mean acc. |
---|---|---|---|---|---|---|
barcode01 | 00 |
00 |
00 |
1098 | 96.8 | 96.5 |
barcode02 | 01 |
01 |
01 |
1253 | 29.8 | 97.5 |
Depth of coverage
Coverage along the individual amplicon, (use the dropdown menu to view the plots for the individual amplicons).