https://github.com/tseemann/phastaf
Identify phage regions in bacterial genomes for masking purposes
https://github.com/tseemann/phastaf
bacteria bioinformatics genomics phage
Last synced: about 1 month ago
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Identify phage regions in bacterial genomes for masking purposes
- Host: GitHub
- URL: https://github.com/tseemann/phastaf
- Owner: tseemann
- License: gpl-3.0
- Created: 2019-05-17T01:37:17.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2019-09-05T00:54:42.000Z (over 5 years ago)
- Last Synced: 2024-06-13T00:03:07.911Z (11 months ago)
- Topics: bacteria, bioinformatics, genomics, phage
- Language: Perl
- Size: 18.4 MB
- Stars: 29
- Watchers: 8
- Forks: 4
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://travis-ci.org/tseemann/phastaf)
[](https://www.gnu.org/licenses/gpl-3.0)
:warning: **THIS SOFTWARE IS STILL IN VERY EARLY DEVELOPMENT!**
# phastaf
Identify phage regions in bacterial genomes for masking purposes
## Introduction
## Quick Start
```bash
% head -n 4 contigs.fna
>AE004092.2 Streptococcus pyogenes M1 GAS, complete genome
TTGTTGATATTCTGTTTTTTCTTTTTTAGTTTTCCACATGAAAAATAGTTGAAAACAATAGCGGTGTCCC
CTTAAAATGGCTTTTCCACAGGTTGTGGAGAACCCAAATTAACAGTGTTAATTTATTTTCCACAGGTTGT
GGAAAAACTAACTATTATCCATCGTTCTGTGGAAAACTAGAATAGTTTATGGTAGAATAGTTCTAGAATT
% phastaf --outdir out contigs.fna
% cat out/phage.bed
AE004092.2 529586 570503 370.1
AE004092.2 778519 821003 370.2
AE004092.2 1189119 1222648 370.3
AE004092.2 1773338 1786887 370.4
```
## Installation
### Homebrew
```
brew install brewsci/bio/phastaf # COMING SOON
phastaf --check
```
Using Homebrew will install all the dependencies for you:
[Linux](http://linuxbrew.sh) or [MacOS](http://brew.sh)
### Conda
```
conda install -c bioconda phastaf # COMING SOON
phastaf --check
```
Learn more about [Bioconda](https://bioconda.github.io/).
### Source
```
git clone https://github.com/tseemann/phastaf.git
./phastaf/bin/phastaf --help
./phastaf/bin/phastaf --check
```
You will need to install all the dependencies manually:
* diamond >= 0.9
* bedtools >= 2.0
* any2fasta >= 0.4
* sort (GNU or BSD)
## Feedback
Please file questions, bugs or ideas
to the [Issue Tracker](https://github.com/tseemann/phastaf/issues)
## License
[GPLv3](https://raw.githubusercontent.com/tseemann/phastaf/master/LICENSE)
## Citation
Not published yet.
## Authors
* Torsten Seemann
* Jake Lacey
* Sharif Shaaban
* Federica Palma
* Rebecca Ji Bengtsson
* Nabil-Fareed Alikhan
* Carlus Deneke