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
73 (13%)
15 (21%)
76.1 k (10%)
1098 96.8 96.5
barcode02
500 (87%)
125 (25%)
701.9 k (90%)
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).

Software versions

Name Version
python 3.8.18
fastcat 0.14.1
ezcharts 0.7.5
dominate 2.8.0
numpy 1.24.4
pandas 2.0.3
pysam 0.21.0
si-prefix 1.2.2
seqkit v2.6.0
porechop 0.2.4
samtools 1.18
minimap2 2.26-r1175
mosdepth 0.3.5
miniasm 0.3-r179
racon 1.5.0
csvtk 0.27.2
medaka 1.11.1

Workflow parameters

Key Value
disable_ping True
out_dir output-ref-free
fastq test_data/fastq-denovo
reads_downsampling_size 500
reference None
sample None
sample_sheet None
analyse_unclassified False
combine_results False
min_read_length 300
max_read_length None
min_read_qual 10
drop_frac_longest_reads 0.05
take_longest_remaining_reads True
min_n_reads 40
number_depth_windows 100
min_coverage 20
basecaller_cfg dna_r10.4.1_e8.2_400bps_sup@v4.2.0
medaka_model None
medaka_target_depth_per_strand 75
force_spoa_length_threshold 2000
spoa_minimum_relative_coverage 0.15
minimum_mean_depth 30
primary_alignments_threshold 0.7
help False
version False
aws_image_prefix None
aws_queue None
threads 4
monochrome_logs False
validate_params True
show_hidden_params False
schema_ignore_params show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf,epi2melabs
wf {'fastcat_stats': True, 'example_cmd': ['--fastq wf-amplicon-demo/fastq', '--reference wf-amplicon-demo/reference.fa'], 'common_sha': 'sha91452ece4f647f62b32dac3a614635a6f0d7f8b5', 'container_sha': 'sha3b6a08c2ed47efd85b17b98762951fffdeee5ba9', 'container_sha_medaka': 'sha61a9438d745a78030738352e084445a2db3daa2a', 'agent': None}