Cargando…

Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2

Optimizing and automating a protocol for 16S microbiome data analysis with QIIME2 is a challenging task. It involves a multi-step process, and multiple parameters and options that need to be tested and determined. In this article, we describe Snaq, a snakemake pipeline that helps automate and optimi...

Descripción completa

Detalles Bibliográficos
Autores principales:	Mohsen, Attayeb, Chen, Yi-An, Allendes Osorio, Rodolfo S., Higuchi, Chihiro, Mizuguchi, Kenji
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Frontiers Media S.A. 2022
Materias:	Bioinformatics
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9580898/ https://www.ncbi.nlm.nih.gov/pubmed/36304319 http://dx.doi.org/10.3389/fbinf.2022.893933

Ejemplares similares

Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks
por: Mohsen, Attayeb, et al.
Publicado: (2019)

The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake
por: Olawoye, Idowu B., et al.
Publicado: (2020)

Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake
por: Thompson, Luke R, et al.
Publicado: (2022)

Recovery of metagenomic data from the Aedes aegypti microbiome using a reproducible snakemake pipeline: MINUUR
por: Foo, Aidan, et al.
Publicado: (2023)

SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing
por: Araújo, Pedro M M, et al.
Publicado: (2019)

MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration
por: Saenz, Carmen, et al.
Publicado: (2022)

Sustainable data analysis with Snakemake
por: Mölder, Felix, et al.
Publicado: (2021)

snHiC: a complete and simplified snakemake pipeline for grouped Hi-C data analysis
por: Gregoricchio, Sebastian, et al.
Publicado: (2023)

Microbiome data analysis with applications to pre-clinical studies using QIIME2: Statistical considerations
por: Rai, Shesh N., et al.
Publicado: (2019)

TargetMine 2022: a new vision into drug target analysis
por: Chen, Yi-An, et al.
Publicado: (2022)

Qiime Artifact eXtractor (qax): A Fast and Versatile Tool to Interact with Qiime2 Archives
por: Telatin, Andrea
Publicado: (2021)

transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
por: Fallon, Timothy R., et al.
Publicado: (2023)

SnakeWRAP: a Snakemake workflow to facilitate automated processing of metagenomic data through the metaWRAP pipeline
por: Krapohl, John, et al.
Publicado: (2022)

Sequanix: a dynamic graphical interface for Snakemake workflows
por: Desvillechabrol, Dimitri, et al.
Publicado: (2018)

FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data
por: Tithi, Saima Sultana, et al.
Publicado: (2018)

Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants
por: Hynst, Jakub, et al.
Publicado: (2019)

Venomix: a simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data
por: Macrander, Jason, et al.
Publicado: (2018)

QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data
por: Estaki, Mehrbod, et al.
Publicado: (2020)

The impact of Docker containers on the performance of genomic pipelines
por: Di Tommaso, Paolo, et al.
Publicado: (2015)

Compi: a framework for portable and reproducible pipelines
por: López-Fernández, Hugo, et al.
Publicado: (2021)

Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
por: Golosova, Olga, et al.
Publicado: (2014)

Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping
por: Ahmed, Zeeshan, et al.
Publicado: (2021)

16S-FASAS: an integrated pipeline for synthetic full-length 16S rRNA gene sequencing data analysis
por: Zhang, Ke, et al.
Publicado: (2022)

A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use
por: Reginato, Marcelo
Publicado: (2022)

MycoVarP: Mycobacterium Variant and Drug Resistance Prediction Pipeline for Whole-Genome Sequence Data Analysis
por: Swargam, Sandeep, et al.
Publicado: (2022)

Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data
por: Armstrong, George, et al.
Publicado: (2022)

High-performance pipeline for MutMap and QTL-seq
por: Sugihara, Yu, et al.
Publicado: (2022)

Large-scale data mining pipeline for identifying novel soybean genes involved in resistance against the soybean cyst nematode
por: Nissan, Nour, et al.
Publicado: (2023)

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
por: Cornwell, MacIntosh, et al.
Publicado: (2018)

Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale
por: Hu, Bin, et al.
Publicado: (2022)

Deep Learning Encoding for Rapid Sequence Identification on Microbiome Data
por: Borgman, Jacob, et al.
Publicado: (2022)

GMEmbeddings: An R Package to Apply Embedding Techniques to Microbiome Data
por: Tataru, Christine, et al.
Publicado: (2022)

CLINE: a web-tool for the comparison of biological dendrogram structures
por: Allendes Osorio, Rodolfo S., et al.
Publicado: (2019)

Evaluation of computational methods for human microbiome analysis using simulated data
por: Miossec, Matthieu J., et al.
Publicado: (2020)

A proof-of-concept pipeline to guide evaluation of tumor tissue perfusion by dynamic contrast-agent imaging: Direct simulation and inverse tracer-kinetic procedures
por: Vignon-Clementel, Irene E., et al.
Publicado: (2023)

DRUID: a pipeline for transcriptome-wide measurements of mRNA stability
por: Lugowski, Andrew, et al.
Publicado: (2018)

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
por: Timme, Ruth E., et al.
Publicado: (2017)

A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species
por: Redelings, Benjamin D., et al.
Publicado: (2017)

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data
por: Chen, Li, et al.
Publicado: (2018)

Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome
por: Miyoshi, Jun, et al.
Publicado: (2018)

Cannot write session to /tmp/vufind_sessions/sess_jf2m0q52udrt5jbk2vm53vrrhu