Help Login Create account

Data released on May 29, 2018

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

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

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.

Contact Submitter

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

Keywords:

metagenomics workflow containerisation docker singularity 

Workflow

http://gigadb.org/images/data/cropped/100459.png

Funding:

  • Funding body - Medical Research Council
  • Award ID - MR/M004422/1

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
ReadmeTEXT1.28 KB2018-05-25
mixed archivearchive32.87 KB2018-05-25
Displaying 1-2 of 2 File(s).

History:

+

Other datasets you might like: