1.workflows-metagenome-isolates.md

implemented workflows and platforms for metagenomes

• [Aviary] - [Python, v0.9.2, 2024.09] - [a snakemake pipeline for assembly, binning, annotation, and strain diversity analysis.]
• [MAG] - [Nextflow, v3.0.3, 2024.8] - [2022.2, NAR Genom Bioinform] - nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.
• [MetaWRAP] - [Shell/Python, v1.3, 2020.08] - [2018.09, Microbime] - [MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis.]
• [VEBA] - [Python, v2.3.0, 2024.9] - [2022.10, BMC Bioinformatics] - VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes.
• [ATLAS] - [Python, v2.19.0, 2024.7] - [2020.6, BMC Bioinformatics] - ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.
• [anvi'o] - [Win/MacOS/Linux, v8, 2023.09] - [2020.12, Nat Microbiol] - [Community-led, integrated, reproducible multi-omics with anvi’o.]
• [nano-rave] - [Nextflow, v1.0.0, 2023.01] - [2023.11, Nat Microbiol] - [Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana.]
• [metagWGS] - [Nextflow, v2.4.2, 2023.6] - [2024.9, bioRxiv] - metagWGS, a comprehensive workflow to analyze metagenomic data using Illumina or PacBio HiFi reads.
• SqueezeMeta - [C/C++/Python/Perl, v1.6.5, 2024.8] - [2019.1, Front Microbiol] - [SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline]
• slamM - [Snakemake]
• [CAT_pack] - [Python, v6.0.1, 2024.3] - [2019.10, Genome Biol] - [Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT.]
• [Metagenomics-Toolkit] - [Nextflow, v0.4.5, 2024.10] - [2024.10, bioRxiv] - [Metagenomics-Toolkit: The Flexible and Efficient Cloud-Based Metagenomics Workflow featuring Machine Learning-Enabled Resource Allocation]

implemented workflows and platforms for isolates

• [Bactopia] - [Nextflow/Perl, v3.1.0, 2024.9] - [2020.8, mSystems] - [Bactopia: a flexible pipeline for complete analysis of bacterial genomes.]
• ASA³P - [Groovy/JS, v1.3.0, 2020.5] - [2020.5, PLoS Comput Biol] - [ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates.]
• [microPIPE] - [html tutorial Nextflow, step by step] - [2021.6, BMC Genomics] - [MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.]
• AQUAMIS - [Python/Shell, v1.4.2, 2024.6] - [2021.4, Genes] - [Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS.]
• Nullarbor - [Perl, v1.41, 2018.6] - [Pipeline to generate complete public health microbiology reports from sequenced isolates.]
• [ProkEvo] - [jupyter tutorial] - [2021.5, PeerJ] - [ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.]
• [Public Health Bioinformatics] - [WDL, v2.2.1, 2024.9] - [2023.7, Microbial Genomics] - [Accelerating Bioinformatics Implementation in Public Health.] - [TheiaCoV(viral), TheiaProk(bacterial)]
• [Public Health Bioinformatics] - [WDL, v2.2.1, 2024.9] - [2023.8, Front. Public Health] - [TheiaEuk: A Species-Agnostic Bioinformatics Workflow for Fungal Genomic Characterization.]
• [rMAP] - [Shell/Python, tutorial] - [2021.6, Microbial Genomics] - [rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data.]
• [TORMES] - [Shell, v1.3.0, 2021.8] - [2019.4, Bioinformatics] - [TORMES: an automated pipeline for whole bacterial genome analysis.]
• [Hybracter] - [Python, v0.10.0, 2024.10] - [2024.5, Microbial Genomics] - [Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies.]

others

• KiNext - [A pipeline for protein kinase identification, classification and phylogeny.]