simroux/iphop repository overview

iPHoP stands for integrated Phage Host Prediction. It is an automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences.

The pipeline can be broken down into 6 main steps:

A: Step 1: Running individual host prediction tools

• Phage-based tool: * RaFAH (https://doi.org/10.1016/j.patter.2021.100274⁠): yield a prediction of host genus with associated score, stored for later (see Step 5)
• Host-based tools: * blastn to host genomes. All hits with ≥ 80% identity and ≥ 500bp are considered. Hits covering ≥ 50% of the "host" contig length are ignored as these often derive from contigs (nearly) entirely viral, and can easily be contaminant in genomes or MAGs and thus not reliable for host prediction * blastn to CRISPR spacer database. All hits with up to 4 mistmaches are considered. * WIsH (https://doi.org/10.1093/bioinformatics/btx383⁠) : host association based on k-mer composition similarity between virus and host genome * VHM - s2* similarity (https://doi.org/10.1093/nar/gkw1002⁠ / https://doi.org/10.1093/nargab/lqaa044⁠): host association based on k-mer composition similarity between virus and host genome * PHP (https://doi.org/10.1186/s12915-020-00938-6⁠): host association based on k-mer composition similarity between virus and host genome

B: Step 2: Collect all scores and all distances between hits for host-based tools * Distance between two potential hosts, i.e., two hits for a given tool and a given query virus, is based on the GTDB trees (https://doi.org/10.1093/nar/gkab776⁠)

C: Steps 3 and 4: Compile an organized list of hits for each virus - tool - candidate host combination * For each hit, the top other hits from the same virus with the same tool are compiled and organized according to the distance between the base hit host and the other hit host (see step 2) * These series of hits are used as input for automated classifiers to derive a score for the given virus - candidate host pair * This enables the evaluation of every potential host (every hit) when considering the context of the top hits obtained for this virus

D: Step 5: Derive 3 scores for host-based tools for each virus - candidate host combination * The top scores based only on blast or crispr matches are retained, as these methods can be reliable enough by themselves for host prediction * A third score is obtained by considering all scores from all individual classifiers (see step 4), i.e. taking into account all 5 host-based methods

E: Step 6: Calculate a composite score for each virus - candidate host genus combination integrating host-based and phage-based signals * The 3 host-based scores (see step 5) are then considered alongside the phage-based score (RaFAH - https://doi.org/10.1016/j.patter.2021.100274⁠) to obtain a single score for all pairs of virus - candidate host genus.

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*** Copyright Notice ***

Integrated Phage-Host Prediction tool (iPHoP) Copyright (c) 2022, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at [email protected]⁠.

NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit others to do so.

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*** License Agreement ***

GPL v3 License

Integrated Phage-Host Prediction tool (iPHoP) Copyright (c) 2022, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/⁠.