genomicepidemiology
by genomicepidemiology (Organization)
Most Popular
Downloads
Usage Instructions
To install packages from this channel, use the channel temporarily with conda or add it to your .condarc file for configured ongoing access. Learn more
- Temporary
- Configured
Packages
| Name | Latest Version | Summary | Updated | License |
|---|
| kma | 1.4.18 | KMA is mapping a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. | Mar 25, 2025 | Apache-2.0 |
| nanomgt | 1.5.0 | NanoMGT - Nanopore Marker Gene Typer | Mar 25, 2025 | Apache-2.0 |
| cgphylo | 1.0.0 | CGPhylo - core genome phylogenetics | Mar 25, 2025 | Apache-2.0 |
| fqgrep | 0.0.3 | fqgrep greps sequences files against a file of sequence identifiers given through -f/--file. For practical reasons you might want to add fingerseq to your path, this is usually done with: | Mar 25, 2025 | Apache-2.0 |
| cgeisolate | 1.1.9 | CGE isolate pipeline | Mar 25, 2025 | Apache-2.0 |
| cgemetagenomics | 1.1.6 | CGE metagenomics pipeline | Mar 25, 2025 | Apache-2.0 |
| kmergenetyper | 1.2.4 | Kmergenetyper test. | Mar 25, 2025 | Apache-2.0 |
| cgevirus | 1.1.9 | CGE Virus Pipeline | Mar 25, 2025 | Apache-2.0 |
| kgt_mlst | 1.0.13 | kgt_mlst test. | Mar 25, 2025 | Apache-2.0 |
| cgmlstfinder | 1.1.5 | Core genome Multi-Locus Sequence Typing cgMLSTFinder runs KMA [1] against a chosen core genome MLST (cgMLST) database and outputs the detected alleles in a matrix file. | Mar 25, 2025 | Apache-2.0 |
| spatyper | 1.0.0 | The spaTyper service predicts the Staphylococcus aureus spa type from genome sequences. | Mar 25, 2025 | Apache-2.0 |
| cgecore | version | cgecore test. | Mar 25, 2025 | Apache-2.0 |
| cgeutil | 1.0.6 | CGE isolate pipeline | Mar 25, 2025 | Apache-2.0 |
| mlst | 2.0.9 | The MLST service contains one python script mlst.py which is the script of the lates version of the MLST service. The method enables investigators to determine the ST based on WGS data. | Mar 25, 2025 | Apache-2.0 |
| ccphylo | 0.8.4 | CCPhylo enables phylogenetic analysis of samples based on overlaps between nucleotide created by e.g. KMA. Input file(s) may be given as non-option arguments succeding all options. | Mar 25, 2025 | Apache-2.0 |
| choleraefinder | 1.0.0 | The CholeraeFinder service contains one python script choleraefinder.py which is the script of the latest version of the CholeraeFinder service. CholeraeFinder identifies important genes in total or partial sequenced isolates of Vibrio Choleraes, and attempts to describe the specimen. | Mar 25, 2025 | Apache-2.0 |
| virulencefinder | 2.0.4 | VirulenceFinder service contains one python script virulencefinder.py which is the script of the latest version of the VirulenceFinder service. VirulenceFinder identifies viruelnce genes in total or partial sequenced isolates of bacteria - at the moment only E. coli, Enterococcus, S. aureus and Listeria are available. | Mar 25, 2025 | Apache-2.0 |
| toxfinder | 1.0.0 | ToxFinder service. | Mar 25, 2025 | Apache-2.0 |
| fingerseq | 0.1.0 | fingerseq extracts basic information about sequence samples, such as the predicted technology, phred scale and whether the sample is paired end. | Mar 25, 2025 | Apache-2.0 |