Assembly and binning of metagenomes
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Updated
Aug 22, 2024 - Nextflow
Assembly and binning of metagenomes
A complete pipeline for metagenomic analysis
Software for prediction of plasmid sequences in metagenomic assemblies
Minimum Information about any (X) Sequence” (MIxS) specification
MetaCarvel: A scaffolder for metagenomes
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
FOCUS: An Agile Profiler for Metagenomic Data
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
Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
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.
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
An algorithm for recovering haplotypes from metagenomes
A few scripts to help with the installation of MetaErg, the contig/bin annotation pipeline
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
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
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.
Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination
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.
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