https://github.com/lczech/ratatosk
Snakemake pipeline for phylogenetic placement of metagenomic sequences
Science Score: 13.0%
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Low similarity (11.1%) to scientific vocabulary
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Repository
Snakemake pipeline for phylogenetic placement of metagenomic sequences
Basic Info
- Host: GitHub
- Owner: lczech
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Size: 1.28 MB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Snakemake pipeline for phylogenetic placement of metagenomic sequences.
Advantages:
- Simplicity: Only expects your files (and settings), and runs everything for you.
- Interoperability: Takes care of file format (in)compatibility between tools.
- Scalability: Works from single files to large datasets, also in cluster environments.
This pipeline is meant for worry-free single-stop placement to run analyses on your data. We recommend to use it in combination with the excellent PEWO workflow. PEWO determines the best tools and settings to be used for accurate placement – which you can then set in ratatosk to get the best of both worlds: accurate and scalable placement.
Pipeline Overview
Minimal input:
- Reference phylogenetic tree (newick)
- Reference multiple-sequence alignment (fasta or phylip)
- Query sequences to be placed (fasta)
Process and available tools:
- Aligning queries
- ...
- Placing queries
- ...
- Visualization
- ...
Output:
- Placed sequences (jplace)
Getting Started
See the Wiki pages for setup and documentation.
For bug reports and feature requests, please open an issue.
What's in a name?!
In Norse mythology, Ratatosk, the drill-tooth, lives in the world-tree Yggdrasil, to which all of the Nine Worlds are connected. Like our mundane squirrels, Ratatosk enjoys whizzing through Yggdrasil’s many branches – which is also how phylogenetic placement algorithms operate! He is regarded as a troublemaker though, which we hope is a quality that is not reflected in our software.
Owner
- Name: Lucas Czech
- Login: lczech
- Kind: user
- Location: Stanford, USA
- Company: Carnegie Institution for Science
- Website: http://lucas-czech.de
- Twitter: LucCzech
- Repositories: 29
- Profile: https://github.com/lczech
Postdoc in bioinformatics :seedling: and computer scientist :octocat: working on inter-disciplinary ways to save the planet :earth_africa:
GitHub Events
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Last Year
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Lucas Czech | l****h@h****g | 16 |
| Pierre Barbera | p****s@g****m | 5 |
Committer Domains (Top 20 + Academic)
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Last synced: 8 months ago
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Past Year
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