Cargando…

QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data

SUMMARY: Next-generation sequencing (NGS) enables reliable detection of resistance mutations in minority variants of human immunodeficiency virus type 1 (HIV-1). There is paucity of evidence for the association of minority resistance to treatment failure, and this requires evaluation. However, the t...

Descripción completa

Detalles Bibliográficos
Autores principales:	Ssekagiri, Alfred, Jjingo, Daudi, Lujumba, Ibra, Bbosa, Nicholas, Bugembe, Daniel L, Kateete, David P, Jordan, I King, Kaleebu, Pontiano, Ssemwanga, Deogratius
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2022
Materias:	Application Note
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9722223/ https://www.ncbi.nlm.nih.gov/pubmed/36699347 http://dx.doi.org/10.1093/bioadv/vbac089

Ejemplares similares

Short Communication: Choosing the Right Program for the Identification of HIV-1 Transmission Networks from Nucleotide Sequences Sampled from Different Populations
por: Bbosa, Nicholas, et al.
Publicado: (2020)

Phylogenetic Networks and Parameters Inferred from HIV Nucleotide Sequences of High-Risk and General Population Groups in Uganda: Implications for Epidemic Control
por: Bbosa, Nicholas, et al.
Publicado: (2021)

Tau-typing: a Nextflow pipeline for finding the best phylogenetic markers in the genome for molecular typing of microbial species
por: Seabolt, Matthew H, et al.
Publicado: (2023)

HIV-1 drug resistance genotyping success rates and correlates of Dried-blood spots and plasma specimen genotyping failure in a resource-limited setting
por: Omooja, Jonah, et al.
Publicado: (2022)

Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda
por: Bbosa, Nicholas, et al.
Publicado: (2020)

The Molecular Epidemiology and Transmission Dynamics of HIV Type 1 in a General Population Cohort in Uganda
por: Ssemwanga, Deogratius, et al.
Publicado: (2020)

Employing phylogenetic tree shape statistics to resolve the underlying host population structure
por: Kayondo, Hassan W., et al.
Publicado: (2021)

Geniac: Automatic Configuration GENerator and Installer for nextflow pipelines
por: Allain, Fabrice, et al.
Publicado: (2022)

Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines
por: Federico, Anthony, et al.
Publicado: (2019)

nf-gwas-pipeline: A Nextflow Genome-Wide Association Study Pipeline
por: Song, Zeyuan, et al.
Publicado: (2021)

TIminer: NGS data mining pipeline for cancer immunology and immunotherapy
por: Tappeiner, Elias, et al.
Publicado: (2017)

Rates of HIV-1 virological suppression and patterns of acquired drug resistance among fisherfolk on first-line antiretroviral therapy in Uganda
por: Omooja, Jonah, et al.
Publicado: (2019)

RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow
por: Lataretu, Marie, et al.
Publicado: (2020)

nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis
por: West, Charlotte, et al.
Publicado: (2023)

Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021
por: Bbosa, Nicholas, et al.
Publicado: (2022)

FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow
por: Vlasova, Anna, et al.
Publicado: (2021)

scATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data
por: Hu, Kai, et al.
Publicado: (2022)

Main Routes of Entry and Genomic Diversity of SARS-CoV-2, Uganda
por: Bugembe, Daniel Lule, et al.
Publicado: (2020)

NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis
por: Singer, Jochen, et al.
Publicado: (2018)

Air pollution and mobility patterns in two Ugandan cities during COVID-19 mobility restrictions suggest the validity of air quality data as a measure for human mobility
por: Galiwango, Ronald, et al.
Publicado: (2022)

GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data
por: Liu, Xiaochuan, et al.
Publicado: (2020)

nf-rnaSeqCount: A Nextflow pipeline for obtaining raw read counts from RNA-seq data
por: Mpangase, Phelelani T., et al.
Publicado: (2021)

Phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations
por: Bbosa, Nicholas, et al.
Publicado: (2019)

Alternate primers for whole-genome SARS-CoV-2 sequencing
por: Cotten, Matthew, et al.
Publicado: (2021)

Sambamba: fast processing of NGS alignment formats
por: Tarasov, Artem, et al.
Publicado: (2015)

Altools: a user friendly NGS data analyser
por: Camiolo, Salvatore, et al.
Publicado: (2016)

LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data
por: Severson, Alissa L, et al.
Publicado: (2021)

Multiple HIV-1 infections with evidence of recombination in heterosexual partnerships in a low risk Rural Clinical Cohort in Uganda
por: Ssemwanga, Deogratius, et al.
Publicado: (2011)

Orione, a web-based framework for NGS analysis in microbiology
por: Cuccuru, Gianmauro, et al.
Publicado: (2014)

RNF: a general framework to evaluate NGS read mappers
por: Břinda, Karel, et al.
Publicado: (2016)

Effect of HIV-1 Subtypes on Disease Progression in Rural Uganda: A Prospective Clinical Cohort Study
por: Ssemwanga, Deogratius, et al.
Publicado: (2013)

Analysis of the history and spread of HIV-1 in Uganda using phylodynamics
por: Yebra, Gonzalo, et al.
Publicado: (2015)

damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets
por: Marshall, Owen J., et al.
Publicado: (2015)

Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines
por: Hu, Qiang, et al.
Publicado: (2021)

amplimap: a versatile tool to process and analyze targeted NGS data
por: Koelling, Nils, et al.
Publicado: (2019)

Computational MHC-I epitope predictor identifies 95% of experimentally mapped HIV-1 clade A and D epitopes in a Ugandan cohort
por: Bugembe, Daniel Lule, et al.
Publicado: (2020)

In-depth annotation of SNPs arising from resequencing projects using NGS-SNP
por: Grant, Jason R., et al.
Publicado: (2011)

SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
por: Arnold, Christian, et al.
Publicado: (2016)

BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort
por: Chun, Hein, et al.
Publicado: (2019)

Synggen: fast and data-driven generation of synthetic heterogeneous NGS cancer data
por: Scandino, Riccardo, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_ms75c5i7cuni4vjltoe8gge0hk