A complete pipeline for metagenomic analysis

Assembly and binning of metagenomes

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

Software for prediction of plasmid sequences in metagenomic assemblies

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)

Minimum Information about any (X) Sequence” (MIxS) specification

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

An algorithm for recovering haplotypes from metagenomes

PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied annotations of the data sets can not be trusted, and so PARTIE allows automatic separation of the data.

PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.

Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.

This is the codebase for Faucet, described in our manuscript: https://academic.oup.com/bioinformatics/article/34/1/147/4004871, by Roye Rozov, Gil Goldshlager, Eran Halperin, and Ron Shamir

MetaCarvel: A scaffolder for metagenomes

scripts for microbiome analysis

Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination

FOCUS: An Agile Profiler for Metagenomic Data

A few scripts to help with the installation of MetaErg, the contig/bin annotation pipeline

MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.