https://github.com/raw-lab/metaome_stats
Statistical package for metaome denovo assembly results.
https://github.com/raw-lab/metaome_stats
fasta genome metagenome metagenome-assembly metaome-stats metatranscriptomics transcriptomics
Last synced: 18 days ago
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Statistical package for metaome denovo assembly results.
- Host: GitHub
- URL: https://github.com/raw-lab/metaome_stats
- Owner: raw-lab
- License: bsd-3-clause
- Created: 2021-05-17T16:28:31.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2022-10-06T18:31:36.000Z (over 3 years ago)
- Last Synced: 2024-08-08T17:17:19.635Z (over 1 year ago)
- Topics: fasta, genome, metagenome, metagenome-assembly, metaome-stats, metatranscriptomics, transcriptomics
- Language: Python
- Homepage:
- Size: 2.64 MB
- Stars: 2
- Watchers: 2
- Forks: 16
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# Metaome Stats: Calculating denovo assembly statistics from metaomes
================================================
## Installing
- pip installation
`pip install MetaomeStats`
- conda installation
`conda install -c bioconda MetaomeStats`
- source (github)
```bash
git clone https://github.com/raw-lab/metaome_stats
cd metaome_stats
python setup.py
```
-------
## Usage examples
```bash
countAssembly.py -i 100 --fasta ecoli_Miseq_Assembly.fa
```
Main options:
```bash
usage: countAssembly.py -i INTERVAL -f FASTA [-r REF] [-s SIZE] [-h]
required arguments:
-i INTERVAL, --interval INTERVAL
interval size in # of residues
-f FASTA, --fasta FASTA
fasta file or folder
optional arguments:
-r REF, --ref REF reference genome
-s SIZE, --size SIZE reference genome size
-h, --help
```
-------
## Input formats
- FASTA files without quality scores (.fasta, .fa, .fna, .ffn format)
-------
## Citing Metaome Stats
If you are publishing results obtained using Metaome Stats, please cite:
## CONTACT
-------
The informatics point-of-contact for this project is [Dr. Richard Allen White III](https://github.com/raw-lab).
If you have any questions or feedback, please feel free to get in touch by email.
Dr. Richard Allen White III: [mailto](mailto:rwhit101@uncc.edu)
Jose Figueroa: [mailto](mailto:jlfiguer@uncc.edu)
Or [open an issue](https://github.com/raw-lab/metaome_stats/issues).