LifeWatch ERIC Metadata Catalogue
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
Identification
- Date ( Publication )
- 2021-04-01
- Date ( Creation )
- 2019-07-04
- Status
- Under development / Pre operational
- Version
- 1.0
- 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
- 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
- Description
- Sequences files downloaded from ENA in a standard format.
- Function
- Input file
- Operation name
- Final_table.tsv
- 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
- 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
- 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/
