https://github.com/aroneys/cross_db_analysis
Compare singleM databases formed from reads, assemblies and bins
Science Score: 13.0%
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Low similarity (2.4%) to scientific vocabulary
Last synced: 10 months ago
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Repository
Compare singleM databases formed from reads, assemblies and bins
Basic Info
- Host: GitHub
- Owner: AroneyS
- Language: Python
- Default Branch: master
- Size: 112 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Created almost 5 years ago
· Last pushed over 4 years ago
Metadata Files
Readme
README.md
Find elusive but prevalent OTUs (i.e. common but unbinned organisms)
Inputs: SingleM Databases
SingleM databases created with combined reads, bins and, optionally, assemblies.
Outputs: Database or CSV file
Database containing table with row for each OTU present in reads. Each row has taxonomy, marker_id, sum(coverage) and flags indicating if the OTU is present in the bins or assemblies and if not, the taxonomy of the nearest bin/assembly OTU.
Steps
- Load output database as SQLITE3 database (as temporary database if unspecified).
- ATTACH reads, assemblies and bins databases.
- CREATE summary tables for each database, deduplicating taxonomy and summing coverage.
- CREATE compare table listing reads OTUs and whether they are present in bins/assemblies.
- Output list of elusive but prevalent OTUs.
- Genus/Species resolution
- High max(sum(coverage)) across marker genes
- No matching bins
Owner
- Name: Samuel Aroney
- Login: AroneyS
- Kind: user
- Website: https://aroneys.github.io/
- Twitter: aroney_samuel
- Repositories: 11
- Profile: https://github.com/AroneyS
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