Software for prediction of plasmid sequences in metagenomic assemblies

Fast and Memory Efficient Genome Sketching via HyperLogLog, HyperMinHash and UltraLogLog

A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.

Teaching materials for SymbNET course: from MAGs to GEMs

ViBE: a hierarchical BERT model to identify viruses using metagenome sequencing data

Software to identify plasmid sequence data from metagenome using logistic regression and Minhash

Axolotl is a Python library for scalable genome analysis, addressing the gap in tools for handling the rapid growth of genomic data with easy parallel processing.

Software to identify known plasmid sequence from metagenomic assembly using Minhash

Using a universal reference database, mixed assemblies, and cutting-edge software to give you the quantitative community phylogeny, a complete community functional analysis, and many strain(ish)-level high-quality bins.

Statistical package for metaome denovo assembly results.

metaSMASH - a scalable fork of antiSMASH for metagenome-scale biosynthetic gene cluster (BGC) mining

OptTaxPro: Optimized Taxonomic Profiling of microbiome using full-length 16S rRNA sequences

Synthetic PHasE Rate Estimator by single metagenome sequence

clutering of MAGs (metagenome assembled genomes) into MGS (metagenomic species)

Growth Rate Index Calculater wrapped by CWL

CAMISIM-BrokenStick is a fork of CAMISIM that implements a broken stick model for substrain abundance simulation.

rplB/rpsC targeted analyses with shotgun metagenomes

taxprofilerVAT (formerly nf-core/taxprofiler) is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data.

Nextflow pipeline incorporating the TRACS alignment step alone

Shotgun metagenomic analysis pipeline for SGE