SFB genomes and annotations

This dataset contains sequence files for a Metagenome Assembled Genome (MAG) from human metagenomes, as well as 5 SFB reference genomes:

• GCF_000270205 Candidatus Arthromitus sp. SFB-mouse-Japan
• GCF_000283555 Candidatus Arthromitus sp. SFB-rat-Yit
• GCF_000284435 Candidatus Arthromitus sp. SFB-mouse-Yit
• GCF_000709435 Candidatus Arthromitus sp. SFB-mouse-NL
• GCF_001655775 Candidatus Arthromitus sp. SFB-turkey isolate UMNCA01

The dataset consists of 8 gzipped tar archives. Here's brief summary of their contents:

• sfb_abundance: Counts of mapped reads and normalized counts for each contig in 825 samples (see sfb_map) Files named 'raw_counts' are number of reads assigned to each contig while files named 'tpm' are counts normalized to Transcripts Per Million. The 'percontig' files show numbers per contig while raw_counts.tab and tpm.tab files have counts summed for each genome.
• sfb_annotations: Annotation files, from running the prokka pipeline on the genomes and subsequently eggnog-mapper, pfam_scan and dbCAN.
• sfb_checkm: Results from running 'checkm lineage_wf' on the genomes.
• sfb_collated: Collated counts of annotations in each genome.
• sfb_fastani: Results from running fastANI on the genomes, with subsequent clustering of genomes based on 75% overlap and 95% ANI.
• sfb_gtdb: Results from the 'gtdbtk classify_wf' on the genomes. This shows how the genomes are classified against the Genome Taxonomy Database (release86).
• sfb_gtdb_denovo: Phylogeny as created using the following command on the genomes.

gtdbtk de_novo_wf --bac120_ms --outgroup_taxon p__Patescibacteria -x .fna --cpus 20 --rnd_seed 123

• sfb_map: Results from mapping reads from 825 samples to the 6 genomes. Reads were aligned using bowtie2 with '--very-sensitive --no-unal' settings and '--score-min C,0,0' to only report reads aligning without mismatches.Output was sorted by position and duplicates removed using MarkDuplicates of the picard tools suite. The archive contains a single merged bam file ('sfb.bam') where each sample has been assigned a ReadGroup inferred from its file name.