Full Report
Date and Time: {{ date_time }}
Mode: {{ mode }}
Configuration Details
{% if config.DATA is defined %}
{% endif %}
{% if config.ALL_CHROMOSOMES is defined %}
{% endif %}
{% if config.HAPLOTYPES is defined %}
{% endif %}
{% if config.BUSCO_DATASET is defined %}
{% endif %}
{% if config.ASSEMBLY_CHROMOSOMES is defined %}
{% endif %}
{% if config.SPECIES is defined %}
{% endif %}
{% if config.FLANKING_GENES is defined %}
{% endif %}
{% if config.RSS_LAYOUT is defined %}
{% endif %}
{% if config.RSS_LENGTH is defined %}
{% endif %}
{% if config.RSS_MERS is defined %}
{% endif %}
Data
-
{% if config.DATA.assembly is defined %}
- Assembly input: {{ config.DATA.assembly }}
- Library: {{ config.DATA.library }} {% else %} Nanopore:
- {{ config.DATA.ORIGINAL.nanopore }}
- {{ config.DATA.MOVED.nanopore }} Pacbio:
- {{ config.DATA.ORIGINAL.pacbio }}
- {{ config.DATA.MOVED.pacbio }} {% endif %}
Chromosomes
-
{% for chromosome in config.ALL_CHROMOSOMES %}
- {{ chromosome }} {% endfor %}
Haplotypes
-
{% for haplotype in config.HAPLOTYPES %}
- {{ haplotype }} {% endfor %}
BUSCO Dataset
- {{ config.BUSCO_DATASET }}
Assembly Chromosomes
-
{% for assembly_chromosome in config.ASSEMBLY_CHROMOSOMES %}
- {{ assembly_chromosome }} {% endfor %}
Species
- Name: {{ config.SPECIES.name }} {% if config.SPECIES.genome is defined %}
- Genome: {{ config.SPECIES.genome }} {% endif %}
- Cell: {{ config.SPECIES.cell }}
Flanking Genes
-
{% for gene in config.FLANKING_GENES %}
- {{ gene }} {% endfor %}
RSS Extraction
-
{% for gene, rss_types in config.RSS_LAYOUT.items() %}
- {{ gene }}
-
{% for rss_type, orientations in rss_types.items() %}
- {{ rss_type }}
- +: {{ orientations["+"] }}
- -: {{ orientations["-"] }}
{% endfor %}
{% endfor %}
- {{ rss_type }}
RSS Heptamer and nonamer lengths
-
{% for length, value in config.RSS_LENGTH.items() %}
- {{ length }}: {{ value }} {% endfor %}
RSS Heptamer and nonamer
-
{% for length, mers in config.RSS_MERS.items() %}
- {{ length }}
-
{% for mer in mers %}
- {{ mer }} {% endfor %}
{% endfor %}
Quality control data
{% for folder in qc_data.keys() %}
{% for folder, files in qc_data.items() %}
{{ folder|capitalize }}
{% endfor %}
File | Format | Type | Num Seqs | Sum Len | Min Len | Avg Len | Max Len |
---|---|---|---|---|---|---|---|
{{ row.file }} | {{ row.format }} | {{ row.type }} | {{ row.num_seqs }} | {{ row.sum_len }} | {{ row.min_len }} | {{ row.avg_len }} | {{ row.max_len }} |
Assembly data (QUAST)
{% for folder in quast_data.keys() %}
{% for folder, data in quast_data.items() %}
{{ folder|capitalize }}
{% endfor %}
{{ column }} | {% endfor %}
---|
{{ value }} | {% endfor %}
Assembly PDFs
{% for pdf in data.pdfs %}
{% endfor %}
BUSCO Data
{% for chromosome in busco_data.keys() %}
{% for chromosome, haplotypes in busco_data.items() %}
{{ chromosome|capitalize }}
{% endfor %}
Haplotype | Single BUSCOs | Fragmented BUSCOs | Duplicates BUSCOs | Missing BUSCOs |
---|---|---|---|---|
{{ haplotype|capitalize }} | {{ metrics['Single BUSCOs'] }} | {{ metrics['Fragmented BUSCOs'] }} | {{ metrics['Duplicates BUSCOs'] }} | {{ metrics['Missing BUSCOs'] }} |
Extracted regions
Sample Name | Region Name | Haplotype | Length (bps) |
---|---|---|---|
{{ row.sample_name }} | {{ row.region_name }} | {{ row.haplotype }} | {{ row.length }} |
RSS MEME sequence motifs
{% for branch in rss_meme_data.keys() %}
{% for branch, types in rss_meme_data.items() %}
{{ branch.split('_')[0] | capitalize }}
{% endfor %}
{% for type in types.keys() %}
{% for type, logos in types.items() %}
{{ type }}
{% endfor %}
{% for logo in logos %}
{% endfor %}
{% endfor %}
{{ logo.folder | replace('_', ' ') }}
Annotation Summary
{% if annotation_summary_100_plus %}Identified known segments
{% for region in annotation_summary_100_plus|groupby('Region') %}
{% for region, rows in annotation_summary_100_plus|groupby('Region') %}
{{ region.grouper }}
{% endfor %}
Region | Haplotype | Function | Segment | Amount |
---|---|---|---|---|
{{ row.Region }} | {{ row.Haplotype }} | {{ row.Function }} | {{ row.Segment }} | {{ row.Count }} |
Identified novel segments
{% for region in annotation_summary_plus|groupby('Region') %}
{% for region, rows in annotation_summary_plus|groupby('Region') %}
{{ region.grouper }}
{% endfor %}
Region | Haplotype | Function | Segment | Amount |
---|---|---|---|---|
{{ row.Region }} | {{ row.Haplotype }} | {{ row.Function }} | {{ row.Segment }} | {{ row.Count }} |