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.

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.