PALACE

PALACE is a computational framework based on deep learning models and conjugate graph theory to assemble high-quality and confident phage genomes from metagenomic sequencing data. PALACE currently supports standard pair-end reads. The assembled phages genomes analyzed in the manuscript are available at Microsoft cloud.

Installation

Install with mamba/conda.(Recommended)

conda create -n palace_env python=3.8
conda activate palace_env
conda install -c delta2cityu -c pytorch -c bioconda -c conda-forge palace
or
#mamba is recommended
mamba create -n palace_env python=3.8
mamba activate palace_env
mamba install -c delta2cityu -c pytorch -c bioconda -c conda-forge palace

Using PALACE

1. Config the config.txt file, here is a demo file.

• fastq1, Read1 paired fastq file.
• fastq2, Read2 paired fastq file.
• phagedb, Phage reference database; the latest phage reference database can be download from without DTR Ref/with checkV Ref.
• protein_db, Phage protein database; the latest phage protein database can be download from here. *gcn_model, Deeplearning model for phage contigs predict; can be download from here
• threads, Threads to be used.
• out_dir, Output directory.
• prefix, Intermediate file prefix, can be sample name.
• ENV_PREFIX, Conda ENV path. Please keep empty if conda ENV is activated.

2. Running PALACE.

• palace --config config.txt

Output

• 01-qc/, fastp output.
• 02-assembly/, Raw assembly result with spades with --meta.
• 03-search/, This directory contains three main intermediate files: hit_seqs.out contains contigs with phage protein. node_scores.out, the second column is the score predicted by deeplearning network. {prefix}_ref_names.txt, contains phage references identified by kmer alignment.
• 04-match/, This directory contains the graph structure of the conjugate graph({prefix}_filtered_graph.txt), the results of the graph decompose({prefix}_all_result.txt).
• 05-furth, This directory contains the local matching result based on the phage reference.
• final_result, This directory contains the final result, final contig paths for phages({prefix}_final.txt), cycle paths for phages({prefix}_cycle.txt), phages fasta(```{prefix}_final.fasta)

Author

PALACE is developed by DeepOmics lab under the supervision of Dr. Li Shuaicheng, City University of Hong Kong, Hong Kong, China. Should you have any queries, please feel free to contact us by gzpan2-c@my.cityu.edu.hk or ruohawang2-c@my.cityu.edu.hk.

License

This project is licensed under the MIT License - see the LICENSE.txt file for details.