Overview ¶
The latest MGnify analysis service (version 5. 0) offers specialised workflows for three different data types: amplicon, raw metagenomic / metatranscriptomic reads, and assembly. Each workflow is defined in common workflow language ( CWL). ( MGnify v5. 0 CWL repository)
All databases are available from an FTP link
The software and databases used for the various processing steps and analyses are listed in the following table. Software, Databases and Versions used by MGnify: ¶
Tool/Database
Version
Purpose
Amplicon
Raw reads
Assemblies
SeqPrep
1. 2
Merging paired end reads
Yes
Trimmomatic
0. 36
Quality control
Biopython
1. 74
bedtools
2. 28. 0
SSU/LSU rRNA masking for ITS
Easel
0. 45h
Sequence extraction
Infernal
1. 1. 2
RNA prediction
Rfam
13. 0
Identification of SSU/LSU rRNA and other ncRNA
MAPseq
1. 2. 3
Taxonomic assignment of SSU/LSU rRNA and ITS
Kronatools
2. 7. 1
Visualisation of taxonomic analyses
biom-format
2. 6
Formatting of taxonomic analyses
mOTUs2
2. 5. 1
Phylogenetic marker gene based taxonomic profiling
FragGeneScan
1.
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– this is why most of the talk about these standards is related to companies and their registration, certification, and accreditation. Certification vs. Registration
When you want to say that a company has implemented a standard (e. g., an Information Security Management System according to ISO 27001), has successfully completed the certification audit, and the certification body has issued the certificate, you would normally call this registration or certification. In North America, the term "registration" is most commonly used, while in the rest of the world it is usually called "certification. " So, is there a difference? Technically, yes; but essentially, no. Certification is when a certification body issues the certificate proving that a company is compliant with a standard; registration is when this certificate is registered with the certification body. So, basically, it comes down to the same thing – a company got a certificate that is formally recognized. By the way, the International Organization for Standardization recommends usage of the term "certification" (see the ISO's explanation here), so I'll use this term from this point forward in this article.