Phage prediction tools to include

[replikation]

List of Tools

Implement?

• VirMiner(Mining, analyzing, and integrating viral signals from metagenomic data)

  • Paper
  • Docker file created

• VirMine (viral sequences from metagenomes)

  • Paper
  • docker available, however, a full pipeline that also does read qc and assembly (spades)
  • but users can supply either raw Illumina sequencing reads (single-end or paired-end) or assembled contigs/scaffolds
  • Docker file created

• PhaMers (Phage k-mers)

  • Paper
  • input: dir where fasta-file | *.fasta is located
  • output: dir: phamer_output/phamer_scores.csv
  • no database
  • Docker file created

• PhiSpy

  • paper
  • phispy support
  • Docker file created

• FastViromeExplorer

  • paper
  • paired end ?
  • databse needed see link
  • Docker file created

• ViromeScan ?

• vConTACT could be interesting to run on final selected putative phage contigs
  https://peerj.com/articles/3243/

• Virminer

Prophage-tools

• Phaster
• Virsorter
• Phage_Finder
• ProphET
• Prophinder
• PhiSpy
• uv ?? phiweger

other interesting tools

• v.HULK

Not possible to implement

• Pro-Hunter --> no CLI ?
  • paper

[replikation]

@Stormrider935

• Overview of Virus Metagenomic Classification Methods and Their Biological Applications

Martin: klingt cool, hier das paper, die haben so nice DAGs gemacht durch die man sich durch hangeln kann jenachdem o man klinisch arbeitet oder nicht und je nachdem was man predicten will
mein fazit bisher: die tools sind alle ein pain-in-the-ass um sie zum laufen zu bekommen und wie gut das ist was sie predicten... really hard to say

[replikation]

Proposed Docker install routine for a conda recipe would be this.
(dummy code for a tool)

FROM continuumio/miniconda3
ENV VERSION <bioconda-version-of-the-tool>
ENV TOOLNAME <name-of-the-tool>

RUN apt-get update && apt install -y procps && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN conda config --add channels conda-forge && \
    conda config --add channels bioconda && \
    conda config --add channels default

RUN conda install $TOOLNAME=$VERSION && conda clean -a

[replikation]

alternatively link to a Docker file if one exists

[replikation]

added recommendation from martin:

• FastViromeExplorer

also edit:
dded FastViromeExplorer
"In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets."
Scheint ViromeScan zu schlagen, welches man auch noch in die Liste aufnehmen koennte.

[hoelzer]

I added VirMine to the list, just read the paper and sounds interesting

[hoelzer]

added VirMiner (now there is a tool called VirMine and another called VirMiner - nice -.-)

[hoelzer]

vConTACT could be interesting to run on final selected putative phage contigs
https://peerj.com/articles/3243/

[hoelzer]

instead of PhaMers I would suggest to implement PhaMer as suggested here #155