Difference between revisions of "MetaLAFFA"
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MetaLAFFA is a pipeline for annotating shotgun metagenomic data with abundances of functional orthology groups. This process consists of several steps to go from raw FASTQs (with sequencing adapters removed) to functional profiles: | MetaLAFFA is a pipeline for annotating shotgun metagenomic data with abundances of functional orthology groups. This process consists of several steps to go from raw FASTQs (with sequencing adapters removed) to functional profiles: | ||
| − | + | Host read filtering (e.g. removing human DNA) | |
| − | + | Duplicate read filtering | |
| − | + | Quality trimming and filtering | |
| − | + | Mapping reads to genes | |
| − | + | Mapping genes to functional orthology groups (e.g. KOs) | |
| − | + | Aggregating orthologs into higher-level groupings (e.g. pathways) | |
<!--Modules--> | <!--Modules--> | ||
Latest revision as of 13:52, 23 September 2021
Description
MetaLAFFA is a pipeline for annotating shotgun metagenomic data with abundances of functional orthology groups. This process consists of several steps to go from raw FASTQs (with sequencing adapters removed) to functional profiles: Host read filtering (e.g. removing human DNA) Duplicate read filtering Quality trimming and filtering Mapping reads to genes Mapping genes to functional orthology groups (e.g. KOs) Aggregating orthologs into higher-level groupings (e.g. pathways)
Environment Modules
Run module spider metalaffa to find out what environment modules are available for this application.
System Variables
- HPC_METALAFFA_DIR - installation directory
- HPC_METALAFFA_BIN - executable directory