DeePhage Alternatives

Similar projects and alternatives to DeePhage

metaGEM

14 165 6.3 Python DeePhage VS metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
PPR-Meta

1 34 1.8 MATLAB DeePhage VS PPR-Meta

A tool for identifying phages and plasmids from metagenomic fragments using deep learning
WorkOS

workos.com sponsored

The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.
VirusSeeker-Virome

1 16 10.0 Perl DeePhage VS VirusSeeker-Virome

VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.
PhaMers

1 6 10.0 Python DeePhage VS PhaMers

A bioinformatic tool for identifying bacteriophages using machine learning and k-mers
virnet

1 29 0.0 Jupyter Notebook DeePhage VS virnet

VirNet: A deep attention model for viral reads identification
RNN-VirSeeker

1 8 0.0 Python DeePhage VS RNN-VirSeeker

This is a deep learning method for identification of viral contigs with short length from metagenomic data.
virMine

1 18 0.0 Python DeePhage VS virMine
InfluxDB

www.influxdata.com sponsored

Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
MetaRon

1 6 1.8 Python DeePhage VS MetaRon

Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.
Cenote_Unlimited_Breadsticks

1 6 2.7 Shell DeePhage VS Cenote_Unlimited_Breadsticks

DEPRECATED: Discover divergent virus sequences, prune flanking cellular sequences, make basic report
ViraMiner

1 28 10.0 Python DeePhage VS ViraMiner

CNN based classifier for detecting viral sequences among metagenomic contigs

NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a better DeePhage alternative or higher similarity.

Suggest an alternative to DeePhage

DeePhage reviews and mentions

Posts with mentions or reviews of DeePhage. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-12-18.

Bad tools that NEED improvement
11 projects | /r/bioinformatics | 18 Dec 2021

Deephage and PPR-meta: both by the same group. They require MATLAB which makes them tricky on an HPC or cloud system. They both say that if you need to run on several samples concurrently, you must clone the tool to a new directory for each(!). Likely due to temporary files being written to the working directory. Entirely unscalable in that case.