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Lists (25)
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Alignment
Alignment toolsAnnotation
Tools for genome annotationAssembly
Tools for genome assemblyBacteria
Specific tools for bacteria related analysesG4
Quadruplex related toolslongReads
Tools for long readsMapping
Reads mapping toolsMetagenomics
Misc tools
ML
Machine Learning related reposMycobacteria
Niche tools for mycobacteria analysisPangenome
Tools related to pan- and coregenome analysisPhage
Niche tools for phages and virusesPhylogeny
Tools for phylogenyPrograms
Python
Python and Jupyter stuffR
R related reposReads
Tools for reads processingRNA
RNAseq related toolsSnakemake
Snakemake related reposStatistics
Taxonomy
Taxonomy related toolsTerminal
Terminal related stuffVariants
Variant calling and manipulation toolsVisualization
Visualization toolsStarred repositories
a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny
Positron, a next-generation data science IDE
An extremely fast Python linter and code formatter, written in Rust.
WtP: Phage identification via nextflow and docker or singularity
Local version of the phage identification and analysis web server (tool set)
A software for phage tail module recognition based on hidden markov model
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.
A simple and fast anti-censorship tool written in Go
#1 Locally hosted web application that allows you to perform various operations on PDF files
Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
NEAT (NExt-generation Analysis Toolkit) simulates next-gen sequencing reads and can learn simulation parameters from real data.
Foldseek enables fast and sensitive comparisons of large structure sets.
A hybrid assembly and MAG recovery pipeline (and more!)
Package that facilitates pulling database entries from KEGG via its REST API
Python library to handle Gene Ontology (GO) terms
resources for learning bioinformatics