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metaSPAdes assembly pipeline
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Knowledge graph centered on metaSPAdes assembly pipeline with 40 nodes and 135 connections. Top connected: leaf water content, biogeochemical reactions, biogeochemical cycling, nitrogen pollution, Microbial communities across a hillslope-riparian .
Description
Standard metagenomics pipeline involving assembly with MEGAHIT, binning with multiple tools, dereplication, and taxonomic classification using GTDB-tk.
Typical Equipment
- MEGAHIT (v1.3.3)
- MetaBAT2 (v2.12.1)
- MaxBin 2.0 (v2.2.6)
- CONCOCT (v1.0.0)
- CheckM (v1.1.3)
- dRep (v3.1.1)
- GTDB-tk
Output Measurements
- metagenome-assembled genomes
- taxonomic classifications
- completeness estimates
Papers Using This Protocol (4)
article
Metagenome-assembled genomes for oligotrophic nitrifiers From a mountainous gravelbed floodplain
article
Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome
article
Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale
article