metaSPAdes assembly pipeline

Knowledge graph centered on metaSPAdes assembly pipeline with 76 nodes and 258 connections. Top connected: Rocky Mountain Biological Laboratory, Gothic, Crested Butte, Pekania pennanti, The East River, Colorado, Watershed: A mountainous.

Method synopsis

Standard metagenomics pipeline involving assembly with MEGAHIT, binning with multiple tools, dereplication, and taxonomic classification using GTDB-tk.

Synthesized from method descriptions across 7 papers using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Metagenome-assembled genomes for oligotrophic nitrifiers From a mountainous gravelbed floodplain (2025), Environmental Microbiology. Implementations in other papers (listed below) may differ.

1. Metagenome assembly and binning
   Assemblies and co-assemblies were made using MEGAHIT (v1.3.3) and binned using contigs > 2000 nt and > 2500 nt, respectively, using MetaBAT2 (v2.12.1), MaxBin 2.0 (v2.2.6), and CONCOCT (v1.0.0) with multiple fastq files grouped by surface (50cm depth), middle depth (70-110 cm), and anoxic depths (130-150 cm). Bins were consolidated and filtered using metawrap bin_refinement to be above > 50% completeness and have < 10% contamination as calculated via CheckM (v1.1.3).
   Quantities: Contigs > 2000 nt for assemblies, > 2500 nt for co-assemblies, >50% completeness and <10% contamination thresholdsDuration: Not specifiedConditions: Standard computational processing conditions
   Equipment: MEGAHIT (v1.3.3), MetaBAT2 (v2.12.1), MaxBin 2.0 (v2.2.6), CONCOCT (v1.0.0), CheckM (v1.1.3)
2. MAG dereplication and taxonomic classification
   All MAGs were dereplicated using dRep (v3.1.1) at 98% average nucleotide identity (ANI). Taxonomic classification for each representative MAG was made using the Genome Taxonomy Database toolkit (GTDB-tk) with the database release 07-RS207.
   Quantities: 98% ANI threshold for dereplicationDuration: Not specifiedConditions: Standard computational conditions
   Equipment: dRep (v3.1.1), GTDB-tk, GTDB database release 07-RS207

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 (7)

Species Studied With This Protocol

Places Where Used