Supporting data for "YAMP: a containerised workflow enabling reproducibility in metagenomics research"

Dataset type: Workflow
Data released on May 29, 2018

Visconti A; Martin TC; Falchi M (2018): Supporting data for "YAMP: a containerised workflow enabling reproducibility in metagenomics research" GigaScience Database. http://dx.doi.org/10.5524/100459

DOI10.5524/100459

YAMP is a user-friendly workflow that enables the analysis of whole shotgun metagenomics data while using containerisation 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 Amazon AWS cloud. Although YAMP has been developed to be ready-to-use by non-experts, bioinformaticians will appreciate its flexibility, modularisation, and simple customisation. The YAMP script, parameters, and documentation are available via the github repo.

Additional details

Read the peer-reviewed publication(s):

Visconti, A., Martin, T. C., & Falchi, M. (2018). YAMP: a containerized workflow enabling reproducibility in metagenomics research. GigaScience, 7(7). doi:10.1093/gigascience/giy072

Additional information:

https://github.com/alesssia/YAMP

https://github.com/alesssia/YAMP/wiki

https://hub.docker.com/r/alesssia/yampdocker

https://doi.org/10.5281/zenodo.1068229

Accessions (data included in GigaDB):

BioProject: PRJEB25791
BioProject: PRJEB26333





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMEA1047262261235509synthetic metagenomesynthetic metagenome Description:DNA isolated from simulated oral microbiome, oral_community
Alternative names:ERS2327609
Collection date:43160
SAMEA1047262271235509synthetic metagenomesynthetic metagenome Description:DNA isolated from simulated oral microbiome, oral_community_human_contamination_1
Alternative names:ERS2327610
Collection date:43160
SAMEA1047262281235509synthetic metagenomesynthetic metagenome Description:DNA isolated from simulated oral microbiome, oral_community_human_contamination_5
Alternative names:ERS2327611
Collection date:43160
SAMEA1047262291235509synthetic metagenomesynthetic metagenome Description:DNA isolated from simulated oral microbiome, oral_community_human_contamination_25
Alternative names:ERS2327612
Collection date:43160
SAMEA1047262301235509synthetic metagenomesynthetic metagenome Description:DNA isolated from simulated oral microbiome, oral_community_human_contamination_50
Alternative names:ERS2327613
Collection date:43160
SAMEA1047262311235509synthetic metagenomesynthetic metagenome Description:DNA isolated from simulated oral microbiome, oral_community_human_contamination_80
Alternative names:ERS2327614
Collection date:43160
SAMEA45978311235509synthetic metagenomesynthetic metagenome Description:DNA isolated from simulated oral microbiome, oral_community_no_duplicates
Alternative names:ERS2418541
Collection date:43160
SAMEA45978321235509synthetic metagenomesynthetic metagenome Description:DNA isolated from simulated oral microbiome, oral_community_artificial_duplicates_1
Alternative names:ERS2418542
Collection date:43160
SAMEA45978331235509synthetic metagenomesynthetic metagenome Description:oral_community_artificial_duplicates_5
Alternative names:ERS2418543
Collection date:43160
SAMEA45978341235509synthetic metagenomesynthetic metagenome Description:DNA isolated from simulated oral microbiome, oral_community_artificial_duplicates_20
Alternative names:ERS2418544
Collection date:43160
Displaying 1-10 of 10 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
ReadmeTEXT1.28 KB2018-05-25
mixed archivearchive32.87 KB2018-05-25
Displaying 1-2 of 2 File(s).
Funding body Awardee Award ID Comments
Medical Research Council MR/M004422/1
Date Action
May 29, 2018 Dataset publish
June 15, 2018 readme.txt: additional file attribute added
June 15, 2018 readme.txt: file attribute updated
June 15, 2018 File readme.txt updated
July 9, 2018 Manuscript Link added : 10.1093/gigascience/giy072