PRéPUBLICATION

GETCampy Sequencing protocols v1

2025

Lien de l'article : https://doi.org/10.17504/protocols.io.e6nvw4jpwlmk/v1

Discipline : Sciences biologiques

Auteur(s) : Ben Pascoe, Henry Badji, Madison Goforth, Evangelos Mourkas, Bako Evariste, Isidore Juste O. Bonkoungou, Modeste T Gampene, Marguerite Edith Malatala Nikiema, Barthelemy Sibiri Zoma, Ousman E Bah, Eustacia J Cassell, Abdoulie K Ceesay, Bubcarr E Ceesay, Ousman Ceesay, Bakary Conteh, Lamin Drammeh, Binta Faye, Abdoulie F Jalllow, Fatima Jallow, Ousman Jallow, Saloum Jallow, Pa Modou Joof, Modou Kandeh, Mehrab Karim, Jarra Manneh, Abdou Aziz Ceesay, Ebrima Fofana, Mamud Jallow, Modou B Jarju, Samba Ba, Dodou Sanyang, Demba B Jallow, Mukaila I Alebiosu, Akosua Bonsu Karikari, Atanyiwoen Brusah, Courage KS Saba, Kaisa Haukka, Catherine Matilda Collins, Adrian W. Leach, Polina Levontin, Shani UP Ali, Frances M. Colles, Matthew D. Hitchings, Martín Antonio, Abdul Karim Sesay, Ozan Gundogdu, Jahangir Hossain, Samuel K. Sheppard

Auteur(s) tagués : BONKOUNGOU Isidore Juste Ouindgueta

Renseignée par : BONKOUNGOU Isidore Juste Ouindgueta

Résumé

As part of the GETCampy-Africa project, this protocol provides a modular workflow for extracting, sequencing, and analysing enteric pathogens from stool and environmental samples. It includes short-read (Illumina MiSeq) and long-read (Oxford Nanopore) sequencing methods, enabling hybrid metagenomic approaches for high-resolution genome assembly. DNA extraction protocols support both total community DNA and high molecular weight recovery. Library preparation workflows include Nextera XT (Illumina), rapid barcoding and ligation kits (ONT), and full-length 16S rRNA sequencing for taxonomic profiling. The protocol also outlines hybrid assembly, binning, and quality control steps for metagenome-assembled genomes (MAGs). Designed for field-lab compatibility and resource-limited settings, these methods support genomic surveillance of Campylobacter and other enteric pathogens across Africa.

Mots-clés

Computer science, Computational biology, Biology

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GETCampy Sequencing protocols v1

Résumé

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