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PEMA Runner

This service aims at running PEMA on all the sequences from the samples selected in Step 4 (ARMS Choose and Parameterize) of the ARMS workflow. It additionally requires a parameter file (a tsv file). The service can take some hours to run.

It represents the Step 5.2 of the ARMS Workflow within the Internal Joint Initiative.

Default

Date ( Publication)
2021-04-01
Date ( Creation)
2019-07-04
Status
Under development / Pre operational
Principal investigator
  VLIZ - Katrina Exter

Custodian
  LifeWatch ERIC ICT Core - Antonio José SÁENZ-ALBANÉS

Publisher
  LifeWatch ERIC Service Centre - Lucia Vaira

Principal investigator
  LifeWatch ERIC ICT Core - ICT Core Group

Keywords

metagenomics

Keywords

remote sensing

Keywords

PEMA

Keywords

ARMS

Keywords

IJI

Keywords

data processing

Access constraints
License
Use limitation

License GNU GPLv3

OnLine resource
PEMA: a Pipeline for Environmental DNA Metabarcoding Analysis (

WWW:LINK-1.0-http--link

)
Operation name

Parameter.tsv

Web site

https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/d1a99bb1-7d5f-4338-8dba-58b922ec42b2

Description

It is a tsv file that can be uploaded in order to specify which sequence (which column gene_18S, gene_COI, gene_ITS) is chosen. It is a well-defined template and the user is required to modify certain fields only.

Function

Input file

Operation name

fastq_sequence_files.fastq

Web site

https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/14c96354-a7d4-4304-a6da-7c6c7dd47ca0

Description

Sequences files downloaded from ENA in a standard format.

Function

Input file

Operation name

Final_table.tsv

Web site

https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/0194b74c-5fb7-492e-aefc-c97944ee0e3e

Description

It is a TSV file with a the number of columns that depends on the number of sequences/samples that are processed in the PEMA run. The first column is an ID. The final column contains the species information. The columns in between are for each sequence (each sample) that was processed and contain integers values; the title of these columns is the ENA code of the sequence (the same as in the MasterARMS csv file).

Function

Output file

Operation name

all_sequences_grouped.fasta

Web site

https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/2dacac79-96c7-41d2-932b-adbfe12976d5

Description

It is a fasta file produced when PEMA is run on gene 18S, gene ITS and COI sequences.

Function

Output file

Operation name

pema_analysis_dir.zip

Web site

https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/b81d3f7c-53b7-4bc1-a4ad-52509cc537f2

Description

The output from PEMA is organised into a directory structure that depends on the details in the Parameter.tsv file.

Function

Output file

Operation name

license.txt

Description

It is a new file added per request of the scientists that lists the license of the tool itself and the licenses of the tools used by PEMA Runner.

Function

Output file

Service Category

data analysis

Service Category

data processing

Service Language
eng
Service TRL
TRL 7 – System prototype demonstration in operational environment
Service Helpdesk

https://helpdesk.lifewatch.eu/

Service Training

https://training.lifewatch.eu/resources/?resource=/course/view.php?id=38

Metadata

File identifier
dec7b713-9757-4941-8632-a9ed73a2c4a1 XML
Metadata language
en
Hierarchy level
Service
Metadata Schema Version

1.0

 
 

Overviews

overview
remote sensing.jpg
overview
metagenomics.jpg

Spatial extent

Keywords



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