A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/pangenome analysis pipeline. For information about how to interpret these results, please see the documentation.
/fusion/s3/nf-core-awsmegatests/work/pangenome/work-3d02bd1df79f48b4bfdb4ad95d4ca0d7f6aeb337/c6/4f78ab670b07bd84dc225b72b10bd0
ODGI
Analysis and manipulation of pangenome graphs structured in the variation graph model.URL: https://github.com/pangenome/odgi
Detailed ODGI stats table.
| Sample Name | Length | Nodes | Edges | Paths | Components | A | C | T | G | N | Self Loops Nodes | Unique Self Loops Nodes | % GC | % N |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| scerevisiae8 | 15216041 | 620531 | 839882 | 136 | 15 | 4666015 | 2886273 | 4648388 | 2893866 | 121499 | 3 | 3 | 38.0% | 0.8% |
Sum of path node distances
For each path we iterate from node to node and count the node / nucleotide distance of nodes on the pangenome level normalized by the path length. If a node is reversed, we count the node distance twice.
This value allows you to evaluate the sorting goodness - how linear the graph is.
Mean links length
For each path we iterate from node to node and count the node / nucleotide distance mean_links_length
of nodes within the same path only. We then normalized by the path length.
This value allows you to evaluate the sorting goodness - how linear the graph is.
ODGI Compressed 1D visualization
This image shows a 1D rendering of the built pangenome graph. The graph nodes are arranged from left to right, forming the pangenome sequence. Summarization of path coverage across all paths. A heatmap color-coding from https://colorbrewer2.org/#type=diverging&scheme=RdBu&n=11 is used. Dark blue means highest coverage. Dark red means lowest coverage. The path names are placed on the left. The black lines under the paths are the links, which represent the graph topology.
ODGI 1D visualization
This image shows a 1D rendering of the built pangenome graph. The graph nodes are arranged from left to right, forming the pangenome sequence. The colored bars represent the paths versus the pangenome sequence in a binary matrix. The path names are placed on the left. The black lines under the paths are the links, which represent the graph topology.
ODGI 1D visualization by path position
This shows a 1D rendering of the built pangenome graph where the paths are colored according to their nucleotide position. Light grey means a low path position, black is the highest path position.
ODGI 1D visualization by path orientation
This image shows a 1D rendering of the built pangenome graph where the paths are colored by orientation. Forward is black, reverse is red.
ODGI 1D visualization by node depth
This shows a 1D rendering of the built pangenome graph where the paths are colored according to path depth. Using the Spectra color palette with 4 levels of path depths, white indicates no depth, while grey, red, and yellow indicate depth 1, 2, and greater than or equal to 3, respectively.
ODGI 1D visualization by uncalled bases
This shows a 1D rendering of the built pangenome graph where the paths are colored according to the coverage of uncalled bases. The lighter the green, the higher the 'N' content of a node is.
ODGI 2D drawing
This image shows a 2D rendering of the built pangenome graph.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| EXTRACT_COMMUNITIES | samtools | 1.17 |
| GFAFFIX | gfaffix | 0.1.5b |
| NET2COMMUNITIES | pggb | 0.5.4 |
| ODGI_BUILD | odgi | 0.9.0 |
| ODGI_DRAW_HEIGHT | odgi | 0.9.0 |
| ODGI_DRAW_MULTIQC | odgi | 0.9.0 |
| ODGI_LAYOUT | odgi | 0.9.0 |
| ODGI_SORT | odgi | 0.9.0 |
| ODGI_SQUEEZE | odgi | 0.9.0) |
| ODGI_STATS | odgi | 0.9.0 |
| ODGI_UNCHOP | odgi | 0.9.0 |
| ODGI_VIEW | odgi | 0.9.0 |
| ODGI_VIZ_COLOR | odgi | 0.9.0 |
| ODGI_VIZ_COMPR | odgi | 0.9.0 |
| ODGI_VIZ_DEPTH | odgi | 0.9.0 |
| ODGI_VIZ_INV | odgi | 0.9.0 |
| ODGI_VIZ_POS | odgi | 0.9.0 |
| ODGI_VIZ_UNCALLED | odgi | 0.9.0 |
| PAF2NET | pggb | 0.5.4 |
| SAMTOOLS_FAIDX | samtools | 1.19.2 |
| SEQWISH | seqwish | 0.7.9 |
| SMOOTHXG | smoothxg | 0.8.0 |
| TABIX_BGZIP | tabix | 1.12 |
| WFMASH_MAP_ALIGN | wfmash | 0.10.4 |
| WFMASH_MAP_COMMUNITY | wfmash | 0.10.4 |
| Workflow | Nextflow | 25.10.2 |
| nf-core/pangenome | v1.1.3-g3d02bd1 |
nf-core/pangenome Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/pangenome
Methods
Data was processed using nf-core/pangenome v1.1.3 (doi: 10.5281/zenodo.8202636) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v25.10.2 (Di Tommaso et al., 2017) with the following command:
nextflow run 'https://github.com/nf-core/pangenome' -name nf-core-pangenome-megatest -params-file 'https://api.cloud.seqera.io/ephemeral/hiGehbQWeSeeX1AYYTrE_A.yaml' -with-tower -r 3d02bd1df79f48b4bfdb4ad95d4ca0d7f6aeb337 -profile test_full
References
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
Notes:
- The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
nf-core/pangenome Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/pangenome
Input/output options
- input
- s3://ngi-igenomes/test-data/pangenome/scerevisiae8.fasta.gz
- n_haplotypes
- 8
- outdir
- s3://nf-core-awsmegatests/pangenome/results-3d02bd1df79f48b4bfdb4ad95d4ca0d7f6aeb337
Wfmash Options
- wfmash_map_pct_id
- 90.0
Seqwish Options
- seqwish_sparse_factor
- 0.0
Community
- communities
- true
Institutional config options
- config_profile_description
- Full test dataset to check pipeline function
- config_profile_name
- Full test profile
Generic options
- trace_report_suffix
- 2026-02-17_18-21-02
Core Nextflow options
- configFiles
- /.nextflow/assets/nf-core/pangenome/nextflow.config, /nextflow.config
- launchDir
- /
- profile
- test_full
- projectDir
- /.nextflow/assets/nf-core/pangenome
- revision
- 1.1.3
- runName
- nf-core-pangenome-megatest
- userName
- root
- workDir
- /nf-core-awsmegatests/work/pangenome/work-3d02bd1df79f48b4bfdb4ad95d4ca0d7f6aeb337