Read summary

Contamination

These two plots show mapping summaries that can highlight potential contamination issues.

The first plot shows the percentage of reads that either map to any combined reference sequence or are unmapped.

The second plot breaks down the the alignment numbers into the specific references (host, helper plasmid, Rep-Cap plasmid, and transgene plasmid).

Truncations

This plot illustrates the frequency of start and end positions of alignments that map completely within the transgene plasmid ITR-ITR region, helping to identify potential truncation hotspots.

ITR-ITR coverage

For each transgene reference, sequencing depth is calculated for both forward and reverse mapping alignments.

AAV Structures

The numbers of different of the various AAV transgene genome types identified in the sample(s) are summarised here.

A detailed report containing more granular genome type assignments per read can be found at: `output/<sample_id>/<sample_id>_aav_per_read_info.tsv`

Assigned_genome_type count percentage sample_id
Backbone contamination 6840 68.4000015258789 sample_1
Partial ssAAV 2620 26.200000762939453 sample_1
Full_ssAAV 511 5.110000133514404 sample_1
Unknown 29 0.28999999165534973 sample_1
Assigned_genome_type count percentage sample_id
Backbone contamination 6840 68.4000015258789 sample_2
Partial ssAAV 2620 26.200000762939453 sample_2
Full_ssAAV 511 5.110000133514404 sample_2
Unknown 29 0.28999999165534973 sample_2

Metadata

Key Value
sample sample_1
type test_sample
barcode sample_1
Key Value
sample sample_2
type test_sample
barcode sample_2

Software versions

Name Version
pysam 0.21.0
minimap2 2.26-r1175
seqkit v2.5.1
samtools 1.15.1
bcftools 1.16
bedtools v2.31.0

Workflow parameters

Key Value
help False
version False
fastq test_data/fastq
bam None
ref_host test_data/cell_line.fasta.gz
ref_helper test_data/helper.fasta
ref_rep_cap test_data/repcap.fasta
ref_transgene_plasmid test_data/transgene.fasta
itr1_start 11
itr1_end 156
itr2_start 2156
itr2_end 2286
threads 4
out_dir wf-aav-qc
sample None
sample_sheet None
aws_image_prefix None
aws_queue None
disable_ping False
analyse_unclassified False
basecaller_cfg dna_r10.4.1_e8.2_400bps_sup@v3.5.2
itr_fl_threshold 100
itr_backbone_threshold 20
symmetry_threshold 10
medaka_model None
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
wf {'fastcat_stats': True, 'example_cmd': ['--fastq wf-aav-qc-demo/simulated_reads.fq', '--itr1_end 156', '--itr1_start 11', '--itr2_end 2286', '--itr2_start 2156', '--ref_helper wf-aav-qc-demo/helper.fasta', '--ref_host wf-aav-qc-demo/cell_line.fasta.gz', '--ref_rep_cap wf-aav-qc-demo/repcap.fasta', '--ref_transgene_plasmid wf-aav-qc-demo/transgene.fasta'], 'container_sha': 'shad9d16c965b87a03180c6dc5534ad86c96a5d9cb0', 'common_sha': 'sha1c5febff9f75143710826498b093d9769a5edbb9', 'container_sha_medaka': 'sha61a9438d745a78030738352e084445a2db3daa2a', 'agent': 'cw-ci'}