YAMP: a containerised workflow enabling reproducibility in metagenomics research

Visconti, Alessia; Martin, Tiphaine; Falchi, Mario

doi:10.1101/223016

Cited by 2 publications

(3 citation statements)

References 60 publications

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Section: Methodsmentioning

confidence: 99%

“…Samples were processed with YAMP using the default parameters, as defined in the published YAMP configuration file, and the databases queried during the YAMP execution were deposited on Zenodo [ 63 ]. The Bray-Curtis dissimilarity values were evaluated using the species relative abundances as estimated by YAMP using MetaPhlAn2 [ 40 ] and the vegdist function in the vegan R package (version 2.4.3) [ 64 ].…”

Section: Methodsmentioning

confidence: 99%

“…Snapshots of the source code are available from the GigaScience GigaDB repository [ 67 ]. The Docker/Singularity image can be downloaded and installed from DockerHub [ 68 ]. The databases queried by YAMP during the simulation and real-world case studies are available from Zenodo [ 63 ].…”

Section: Availability Of Supporting Datamentioning

confidence: 99%

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YAMP: a containerized workflow enabling reproducibility in metagenomics research

2018

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YAMP ("Yet Another Metagenomics Pipeline") is a user-friendly workflow that enables the analysis of whole shotgun metagenomic data while using containerization to ensure computational reproducibility and facilitate collaborative research. YAMP can be executed on any UNIX-like system and offers seamless support for multiple job schedulers as well as for the Amazon AWS cloud. Although YAMP was developed to be ready to use by nonexperts, bioinformaticians will appreciate its flexibility, modularization, and simple customization.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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YAMP: a containerized workflow enabling reproducibility in metagenomics research

2018

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Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes

Poulsen¹,

Pamp

Ct³

et al. 2019

Preprint

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15Next generation sequencing technologies have become increasingly used to describe microbial communities. 16 Metagenomics characterization of microbiomes is associated with minimal manipulation during sample 17 processing, which includes sampling, storage, DNA isolation, library preparation and sequencing, before the 18 raw data are obtained. Here we assess the effect of library preparation using a kit with a polymerase chain 19 reaction (PCR) step (Nextera) and two PCR-free kits (NEXTflex and KAPA), and the effect of sequencing 20 platform (HiSeq and NextSeq) on the description of microbial communities in pig feces and sewage. Two pig 21 fecal samples were obtained from different farms and two sewage samples were collected as inlet water at 22 a local wastewater treatment facility. Samples were processed to both perform DNA-isolation immediately 23 upon arrival in the lab and after storage for 64 hours at -80°C, DNA isolation was performed in duplicate. 24We find that both library preparation and sequencing platform had systematic effects on the microbial 25 community description. The effects were at a level that made differentiating between the two pig fecal 26 samples difficult. The sewage samples represented two very different communities and were at all times 27 distinguishable from each other. We find that library preparation and sequencing platform introduced more 28 variation than freezing the samples. The community changes did not seem associated with contamination 29 during processing and distinct patterns connected specific types of organisms with a processing method, but 30it was difficult to generalize between samples. This highlights the need for continuous validation of the effect 31 of sample processing in different types of samples and that all processing steps need to be considered when 32 comparing between studies. We believe standardization of sample processing is key to generate comparable 33data within a study and that comparisons of differently generated data, e.g. in a meta-analysis, should be 34 performed cautiously.35 36

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YAMP: a containerised workflow enabling reproducibility in metagenomics research

Cited by 2 publications

References 60 publications

YAMP: a containerized workflow enabling reproducibility in metagenomics research

YAMP: a containerized workflow enabling reproducibility in metagenomics research

Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes

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