SFB genomes and annotations

Sequence files for a Metagenome Assembled Genome from human metagenomes and 5 reference genomes of Segmented Filamentous Bacteria (SFB) from mouse, rat, and turkey hosts. The dataset includes 8 archives containing genome annotations, quality assessments, taxonomic classifications, and read abundance data from 825 samples. It was authored by John Sundh of Stockholm University.

Use Cases

• Comparative genomics analysis based on the 5 SFB reference genomes and one MAG.
• Taxonomic classification of microbial genomes based on GTDB and CheckM results.
• Abundance profiling of SFB across samples based on mapped read counts from 825 metagenomes.
• Functional annotation analysis based on outputs from prokka, eggnog-mapper, pfam_scan, and dbCAN.
• 16S Amplicon Sequence Variant (ASV) analysis based on the SFB.unoise.vsearch.tsv count table.

Strengths

• Includes 6 distinct genomes (5 reference genomes and one MAG) for comparative analysis.
• Provides annotation data from multiple established bioinformatics pipelines (prokka, eggnog-mapper, pfam_scan, dbCAN).
• Contains abundance data derived from mapping reads from 825 samples, offering a broad survey context.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Last update date is unknown; freshness unverified.

Provenance

Source

John Sundh, Stockholm University

Collection Method

Metagenome assembly, reference genome collection, and bioinformatic processing (prokka, bowtie2, GTDB-Tk, etc.).