Assembly Summary

The table below shows key assembly statistics for each sample, including contig counts, assembly size, read mapping rate, and BUSCO completeness scores where available. Click on any row to display the detailed per-sample results in the sections below.

{% for header in summary_header %} {% endfor %} {% for sample, values in summary_results.items() %} {% for value in values %} {% endfor %} {% endfor %}

Sample	{{header}}
{{sample}}	{{value}}

{% for sample, contigs_dict in analysis.items() %}

Download the final contig sequences for this sample: {{sample}}.fasta.

{% if 'bandage_image' in analysis[sample] %}

Assembly graph

Assembly graph produced by Bandage showing contig connectivity before circularisation. Hover the image to view it in colour.

{% endif %} {% if 'Complete BUSCOs' in summary_header %}

BUSCO completeness

BUSCO assesses genome completeness by searching for a set of near-universal single-copy orthologs. Values show counts of complete (single-copy and duplicated), fragmented, and missing BUSCOs.

{% set busco_start = summary_header.index('Complete BUSCOs') %} {% for i in range(4) %} {% endfor %}

{{ summary_header[busco_start + i] }}	{{ summary_results[sample][busco_start + i] }}

{% endif %} {% if 'checkm' in analysis[sample] %}

CheckM genome quality — {{analysis[sample]['rank']}} (rank: {{analysis[sample]['genus']}})

CheckM estimates genome completeness and contamination by placing the assembly in a reference genome tree and identifying lineage-specific marker genes.

{% for key, value in analysis[sample]['checkm'].items() %} {% endfor %}

{{key}}	{{value}}

{% else %}

CheckM was not run for this sample. Enable it by setting checkm.do: true in the config file.

{% endif %} {% for contig in contigs_dict['contig_order'] %}

{% if 'coverage' in analysis[sample][contig] %}

Sequana coverage

Depth of coverage (DOC) and breadth of coverage (BOC) computed by Sequana. Click the image to open the interactive coverage report for this contig.

{% for key, value in analysis[sample][contig]['coverage'].items() %} {% endfor %}

{{key}}	{{value}}

{% elif contig == contigs_dict['contig_order'][0] %}

Sequana coverage was not run for this sample. Enable it by setting sequana_coverage.do: true in the config file.

{% endif %} {% if 'blast' in analysis[sample][contig] %}

BLAST hits

Top BLAST alignments for this contig against the configured database. For each subject sequence, the hit with the highest bitscore is shown (up to 5 results).

{% for title in analysis[sample][contig]['blast'][0].keys() %} {% endfor %} {% for blast in analysis[sample][contig]['blast'] %} {% for value in blast.values() %} {% endfor %} {% endfor %}

{{title}}
{{value}}

{% elif blast_done %}

BLAST hits

No BLAST hits found for {{contig}}.

{% elif contig == contigs_dict['contig_order'][0] %}

BLAST was not run for this sample. Enable it by setting blast.do: true in the config file.

{% endif %}

{% endfor %}