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All Projects → tseemann → phastaf

tseemann / phastaf

Licence: GPL-3.0 license
Identify phage regions in bacterial genomes for masking purposes

Programming Languages

perl
6916 projects

Labels

bioinformaticsgenomicsbacteriaphage

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Build Status License: GPL v3 Don't judge me

⚠️ THIS SOFTWARE IS STILL IN VERY EARLY DEVELOPMENT!

phastaf

Identify phage regions in bacterial genomes for masking purposes

Introduction

Quick Start

% 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 or MacOS

Conda

conda install -c bioconda phastaf  # COMING SOON
phastaf --check

Learn more about Bioconda.

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

License

GPLv3

Citation

Not published yet.

Authors

  • Torsten Seemann
  • Jake Lacey
  • Sharif Shaaban
  • Federica Palma
  • Rebecca Ji Bengtsson
  • Nabil-Fareed Alikhan
  • Carlus Deneke
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