MetaPhage report
MetaPhage: a nextflow pipeline for phage discovery.
- Demo report
- MetaPhage 0.3.0
- NOTE
- Not all links will work in this online demo. For space reasons, some attachments and plots are not available.
Report generated on 2022-03-31, 13:37
Miner Comparison
vOTUs prediction per miner, performed on consensus sequences (i.e. after dereplication).
Summary Table
vOTUs general statistics. Each violin plots shows the vOTUs abundances per sample. All links will open the violin plot of sample SRR8652861 in the online demo.
Taxonomy Table
Custom vOTUs taxonomy generated over vConTACT outputs. All links will open the violin plot of vOTU_1 in the online demo.
Interactive Plots
Links to the analysis plots. The link will open the relative plot directly on the browser
Alpha Diversity Plots
Links to the alpha diversity plots. The link will open the relative plot directly on the browser
Note: in the demo version all links will open the Chao1 plots
| Metric | Link |
|---|---|
| Observed Chao1 | Alpha_OCS |
| AceSAcSha | Alpha_AAS (!) |
| SimISiFis | Alpha_SIF (!) |
Beta Diversity Plots
Links to the beta diversity plots. The link will open the relative plot directly on the browser
Note: in the demo version all links will open the Jackard plots are disabled
| Metric | Link |
|---|---|
| Bray_2D | Bray_2D |
| Bray_3D | Bray_3D |
| Jaccard_2D | Jaccard_2D (!) |
| Jaccard_3D | Jaccard_3D (!) |
Interesting Files
Not available in the online demo.
| File | Link |
|---|---|
| Count_Table | Count_Table (!) |
| Taxonomy_Table | Taxonomy_Table (!) |
| Philoseq_obj | Phyloseq (!) |
| Philoseq_css_norm_obj | Phyloseq_css_norm (!) |
| vOTUs_multifasta | vOTUs_multifasta (!) |
| vOTUs_proteins | vOTUs_proteins (!) |
| vOTUs_gff | vOTUs_gff (!) |
fastp
fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)
Filtered Reads
Filtering statistics of sampled reads.
Duplication Rates
Duplication rates of sampled reads.
Insert Sizes
Insert size estimation of sampled reads.
Sequence Quality
Average sequencing quality over each base of all reads.
GC Content
Average GC content over each base of all reads.
N content
Average N content over each base of all reads.
Kraken
Kraken is a taxonomic classification tool that uses exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.
Top taxa
The number of reads falling into the top 5 taxa across different ranks.
To make this plot, the percentage of each sample assigned to a given taxa is summed across all samples. The counts for these top five taxa are then plotted for each of the 9 different taxa ranks. The unclassified count is always shown across all taxa ranks.
The total number of reads is approximated by dividing the number of unclassified reads by the percentage of
the library that they account for.
Note that this is only an approximation, and that kraken percentages don't always add to exactly 100%.
The category "Other" shows the difference between the above total read count and the sum of the read counts in the top 5 taxa shown + unclassified. This should cover all taxa not in the top 5, +/- any rounding errors.
Note that any taxon that does not exactly fit a taxon rank (eg. - or G2) is ignored.
Kraken2 and Krona files
Links to the Kraken2 and Krona reports in your local folder. Kraken2 table not available in the online demo. Krona plot links will all open the first sample.
QUAST
QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.
Assembly Statistics
| Sample Name | N50 (Kbp) | N75 (Kbp) | L50 (K) | L75 (K) | Largest contig (Kbp) | Length (Mbp) |
|---|---|---|---|---|---|---|
| SRR8652861 | 3.9Kbp | 1.5Kbp | 2.0K | 8.1K | 269.0Kbp | 55.0Mbp |
| SRR8652914 | 12.9Kbp | 1.6Kbp | 0.2K | 1.4K | 319.4Kbp | 17.4Mbp |
| SRR8652969 | 17.3Kbp | 2.7Kbp | 0.4K | 2.1K | 423.1Kbp | 41.5Mbp |
| SRR8653084 | 11.2Kbp | 2.3Kbp | 1.0K | 4.2K | 466.0Kbp | 61.0Mbp |
| SRR8653090 | 11.8Kbp | 1.8Kbp | 0.3K | 1.6K | 247.5Kbp | 20.5Mbp |
| SRR8653218 | 15.8Kbp | 2.6Kbp | 0.3K | 1.6K | 353.7Kbp | 29.1Mbp |
| SRR8653221 | 5.0Kbp | 1.1Kbp | 1.1K | 7.8K | 352.6Kbp | 52.3Mbp |
| SRR8653245 | 23.3Kbp | 2.5Kbp | 0.3K | 1.9K | 568.6Kbp | 39.5Mbp |
| SRR8653247 | 5.0Kbp | 1.5Kbp | 0.8K | 3.1K | 308.3Kbp | 24.2Mbp |
| SRR8653248 | 4.8Kbp | 1.3Kbp | 0.9K | 4.2K | 844.3Kbp | 30.6Mbp |
Number of Contigs
This plot shows the number of contigs found for each assembly, broken down by length.
