dec7b713-9757-4941-8632-a9ed73a2c4a1 1.0 PEMA Runner 2024-07-05 This service aims at running PEMA. It requires a parameter file (a tsv file). The service can take some time to run. It is part of the ARMS workflow of the Internal Joint Initiative available here: <a href="https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/edf6017e-dc2f-4eec-8248-5a6c5de381b6" target="_blank">https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/edf6017e-dc2f-4eec-8248-5a6c5de381b6</a>. Katrina Exter VLIZ katrina.exter@vliz.be Antonio José SÁENZ-ALBANÉS LifeWatch ERIC ICT Core aj.saenz@lifewatch.eu Lucia Vaira LifeWatch ERIC Service Centre lucia.vaira@lifewatch.eu ICT Core Group LifeWatch ERIC ICT Core ict.coordination@lifewatch.eu https://metadatacatalogue.lifewatch.eu/geonetwork/srv/api/records/dec7b713-9757-4941-8632-a9ed73a2c4a1/attachments/remote%20sensing.jpg remote sensing.jpg metagenomics remote sensing PEMA ARMS IJI data processing GPLv3 Parameter.tsv https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/d1a99bb1-7d5f-4338-8dba-58b922ec42b2 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. Input file fastq_sequence_files.fastq https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/14c96354-a7d4-4304-a6da-7c6c7dd47ca0 Sequences files downloaded from ENA in a standard format. Input file Final_table.tsv https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/0194b74c-5fb7-492e-aefc-c97944ee0e3e 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). Output file all_sequences_grouped.fasta https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/2dacac79-96c7-41d2-932b-adbfe12976d5 It is a fasta file produced when PEMA is run on gene 18S, gene ITS and COI sequences. Output file pema_analysis_dir.zip https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/b81d3f7c-53b7-4bc1-a4ad-52509cc537f2 The output from PEMA is organised into a directory structure that depends on the details in the Parameter.tsv file. Output file license.txt 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. Output file Workflow Studio data analysis data processing https://helpdesk.lifewatch.eu/ https://training.lifewatch.eu/resources/?resource=/course/view.php?id=38 https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/55dfbb63-4304-4fa8-a7b6-17988e0b33df WWW:LINK-1.0-http--link PEMA: a Pipeline for Environmental DNA Metabarcoding Analysis https://my.lifewatch.eu/workflow/create-workflow-from-template/arms-pema-runner WWW:LINK-1.0-http--link Link to the workflow