MultiQC report - Githubissues

NBISweden / Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.

https://www.earthbiogenome.org/

GNU General Public License v3.0

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MultiQC report #83

Open mahesh-panchal opened 9 months ago

mahesh-panchal commented 9 months ago

Need summary report and full report for QC.

Summary report

General
- ToLID
- Species
- Class
- Order
Genome Traits
- Haploid Size
- Haploid Number
- Ploidy
- Sample Sex
EBP Metrics and curation notes
- Table of metrics ?
- Metrics flagged as red ( below EBP standards )
- Curator notes
- Contaminants detected
- Other observations
Data Profile
- Table of Coverage ( HiFi, ONT, Bionano, HiC )
Assembly pipeline
- Tool version table ( Hifiasm, purge_dups, bionano, YaHS )
Curation pipeline
- Tool version table ( GRIT_rapid, HiGlass )
Metrics Table
Hi Contact Map
Kmer Spectra
Blob ( Bubble ) of cov vs gc.

Full report

Table of assembly standards met
Sequence metrics ( from ? )
- Total sequence data
- Sequence distribution
- Expected coverage ( total bases / estimated genome size )
GenomeScope

mahesh-panchal commented 9 months ago

MQC with current workflow only finds:

Busco
Quast

Other tools that may be of interest:

KAT
Kraken
mosdepth
qc3c ( Hi-C)
samtools
sourmash