README.md

Phage-EnrichSeq

Finding phages for phage therapy using Enrichment followed by Differential Genome Amplification.

Getting Started.

Activate enrichseq conda environment with pre-installed dependencies

To setup the conda environment, use the following command once conda is installed locally.

• for linux

conda env create -f environment_linux.yml;

• for mac

conda env create -f environment_mac.yml;

• To activate, use the following always before running EnrichSeq:

conda activate enrichseq;

Download DB

python3 EnrichSeq.py db_build

Running EnrichSeq.

Below are examples using single end and paired end reads. For further usage, please refer to the EnrichSeq Wiki.

• USAGE (single end reads)

python3 EnrichSeq.py enrichseq -1 examples/single_end_reads/simulated_test_reads_illumina.fa -o single_out_example

• USAGE (paired end reads)

python3 EnrichSeq.py enrichseq -1 examples/paired_end_reads/paired_illumina_1.fa -2 examples/paired_end_reads/paired_illumina_2.fa -o paired_out