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phirbo

Predict prokaryotic hosts for phage (meta) genomic sequences

phist

Phage-Host Interaction Search Tool

plasflow

Software for prediction of plasmid sequences in metagenomic assemblies

plasmidhunter

This tool predicts plasmid sequences from genomic and metagenomic assemblies using machine learning.

plasx

PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture

plsdbapi

pprodigal

Python3 wrapper for parallelized gene prediction using Prodigal

prodigal-gv

A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes

pullseq

Utility program for extracting sequences from a fasta/fastq file

rawgraphs-app

A web interface to create custom vector-based visualizations on top of RAWGraphs core

rosettafold-all-atom

scycdb

seeker

shrinksam

C++ program to shrink the SAM file after a read-mapping

sickle

Windowed Adaptive Trimming for fastq files using quality

spacegraphcats

Indexing large assembly graphs -- remember, in space, no one can hear you miao!

spades-contig-graph

a tool for creating a FASTG contig graph from a SPAdes assembly

sphae

NEW!!! Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!

sra-tools

SRA Tools

tango

Taxonomic classification of metagenomic contigs

temperate-phage-active-prophage-detection

detect temperate phage (active prophage) in assembled bacterial genome sequences

trep

Quick get the taxonomy of a genome

ubin

umap

Uniform Manifold Approximation and Projection

useful_scripts

valet

A pipeline for detecting mis-assemblies in metagenomic assemblies.

vibrant

Virus Identification By iteRative ANnoTation

viptreegen

a command line tool for viral proteomic tree generation, part of the ViPTree project: http://www.genome.jp/viptree

viwrap

A wrapper to identify, bin, classify, and predict host-viral relationship for viruses

vpf-tools

Virus Protein Family tools