MGKit: Metagenomics Framework
The aim of this library [1] is to provide a series of useful modules and packages to make it easier to build custom pipelines for metagenomics or any kind of bioinformatics analysis. It integrates other well known python libraries in bioinformatics, like HTSeq, pysam, numpy and scipy.
Documentation is available at https://frubino.github.io Data and scripts used in the documentations are available at [2].
A discussion mailing list is available at mgkit-users.
Papers using MGKit
Rubino, F., Carberry, C., M Waters, S., Kenny, D., McCabe, M. S., & Creevey, C. J. (2017). Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome. The ISME Journal, 1–13. https://doi.org/10.1038/ismej.2016.172
Lambert, B. S., Raina, J. B., Fernandez, V. I., Rinke, C., Siboni, N., Rubino, F., … Stocker, R. (2017). A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities. Nature Microbiology, 2(10), 1344–1349. https://doi.org/10.1038/s41564-017-0010-9
Hitch, T. C. A., Thomas, B. J., Friedersdorff, J. C. A., Ougham, H., & Creevey, C. J. (2018). Deep sequence analysis reveals the ovine rumen as a reservoir of antibiotic resistance genes. Environmental Pollution, 235, 571–575. https://doi.org/10.1016/j.envpol.2017.12.067
Computational haplotype recovery and long-read validation identifies novel isoforms of industrially relevant enzymes from natural microbial communities Samuel M Nicholls, Wayne Aubrey, Arwyn Edwards, Kurt de Grave, Sharon Huws, Leander Schietgat, André Soares, Christopher J Creevey, Amanda Clare bioRxiv 223404; doi: https://doi.org/10.1101/223404
Citing
Rubino, F. and Creevey, C.J. 2014. MGkit: Metagenomic Framework For The Study Of Microbial Communities. . Available at: figshare [doi:10.6084/m9.figshare.1269288].`
a citation is also available using the mgkit.cite() function or using the –cite option on all scripts included. This will ouput the following
Links
1 maintainer
Metadata
1 maintainer
Release files for mgkit 0.5.8
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| mgkit-0.5.8.tar.gz | 11.7 MB | Without provenance | Details for mgkit-0.5.8.tar.gz |
Release files / mgkit-0.5.8.tar.gz
| Download URL | mgkit-0.5.8.tar.gz |
|---|---|
| Size | 11.7 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
fe2537f5446eee6cc7d390e0d94b16fb57f1bee1b549bdef29540721a87d78d6
|
|
BLAKE2b-256 checksum How to use checksums |
d0d653e46dfafa21fb82f29ce1e788eb16f20a6946cabd3d7f8bf92747a40c9b
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.2 importlib_metadata/3.10.0 pkginfo/1.7.1 requests/2.24.0 requests-toolbelt/0.9.1 tqdm/4.51.0 CPython/3.8.8
|
Security for mgkit 0.5.8
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
