Summary

This report contains visualisations of statistics that can help in understanding the results from the wf-alignment workflow. Each section contains different plots or tables, and in general the results are broken down by sample or the reference file to which alignments were made. You can quickly jump to an individual section with the links in the header bar.

2 samples:
barcode01 barcode02

2 reference files:
ERCC.fasta SIRV_isoforms_multi-fasta_170612a.fasta

99 reference sequences:
ERCC-00002 ERCC-00003 ERCC-00004 ERCC-00009 ERCC-00012 ERCC-00013 ERCC-00014 ...

Metric Value Percentage
Detected reference sequences 29
29.3%
Reads 3,999
100.0%
Reads aligned to 'ERCC.fasta' 351
8.8%
Reads aligned to 'SIRV_isoforms_multi-fasta_170612a.fasta' 3,428
85.7%
Unmapped reads 220
5.5%
Bases 3,201,731
100.0%
Metric Value Percentage
Detected reference sequences 27
27.3%
Reads 1,600
40.0%
Reads aligned to 'ERCC.fasta' 225
14.1%
Reads aligned to 'SIRV_isoforms_multi-fasta_170612a.fasta' 1,250
78.1%
Unmapped reads 125
7.8%
Bases 1,252,199
39.1%
Metric Value Percentage
Detected reference sequences 10
10.1%
Reads 2,399
60.0%
Reads aligned to 'ERCC.fasta' 126
5.3%
Reads aligned to 'SIRV_isoforms_multi-fasta_170612a.fasta' 2,178
90.8%
Unmapped reads 95
4.0%
Bases 1,949,532
60.9%

Read and alignment summary statistics

Read quality and length in addition to alignment accuracy and coverage are illustrated in the plots below.

Depth of coverage

This section illustrates the depth of coverage of the reference genomes. The left plot shows coverage vs. genomic position (note that the coordinates on the x-axis are the positions along the concatenated reference including all reference sequences in the respective reference file). The right plot shows the cumulative fraction of the reference that was covered to at least a certain depth.

Read count control

When a file with expected read counts was provided, this plot shows the observed vs. expected counts for each sample / reference sequence combination.

Reference file 'ERCC.fasta':

Software versions

Name Version
python 3.8.18
seqkit v2.6.1
minimap2 2.26-r1175
samtools 1.18
fastcat 0.15.1
mosdepth 0.3.6
ezcharts 0.7.6
pysam 0.21.0
bgzip (htslib) 1.18

Workflow parameters

Key Value
out_dir wf-alignment
fastq test_data/fastq
bam None
references test_data/references
reference_mmi_file None
counts test_data/counts/ERCC_mix1.csv
prefix None
sample None
sample_sheet None
depth_coverage True
analyse_unclassified False
minimap_preset dna
minimap_args None
threads 4
per_read_stats False
store_dir wf-alignment/store_dir