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metaSPAdes assembly pipeline

Subcategory: metagenomics
Standard reference: Hernsdorf et al. (2017)
Papers: 4 | Mentions: 25

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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

2025Environmental Microbiologyusing
article

Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome

2025Microbiomeusing
article

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

2021Microbiomeusing
article

Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock

2019Ecology and Evolutionusing

Species Studied With This Protocol

Nitrososphaera sp.

1 paper

Desulfobacca acetoxidans

Syntrophaceae1 paper

Geobacter spp.

1 paper

Desulfuromonas sp.

1 paper

Thaumarchaeota

1 paper

Bathyarchaeota

1 paper

Euryarchaeota

1 paper

Alphaproteobacteria

1 paper

Gammaproteobacteria

1 paper

Shewanella oneidensis

1 paper

Places Where Used

Colorado River

stream1 paper

Gunnison

study site1 paper

Gunnison River Basin

watershed1 paper

Crested Butte

study site1 paper

Boulder

region1 paper

south-central Colorado

region1 paper

San Joaquin Valley

valley1 paper

Uncompahgre River Basins

watershed1 paper

eastern Tibetan plateau

region1 paper

PLM

study site1 paper