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: <strong>sfb_abundance</strong>: Counts of mapped reads and normalized counts for each contig in 825 samples (see <strong>sfb_map</strong>) 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. <strong>sfb_annotations</strong>: Annotation files, from running the prokka pipeline on the genomes and subsequently eggnog-mapper, pfam_scan and dbCAN. <strong>sfb_checkm</strong>: Results from running 'checkm lineage_wf' on the genomes. <strong>sfb_collated</strong>: Collated counts of annotations in each genome. <strong>sfb_fastani</strong>: Results from running fastANI on the genomes, with subsequent clustering of genomes based on 75% overlap and 95% ANI. <strong>sfb_gtdb</strong>: Results from the 'gtdbtk classify_wf' on the genomes. This shows how the genomes are classified against the Genome Taxonomy Database (release86). <strong>sfb_gtdb_denovo</strong>: Phylogeny as created using the following command on the genomes. <pre><code class="language-bash">gtdbtk de_novo_wf --bac120_ms --outgroup_taxon p__Patescibacteria -x .fna --cpus 20 --rnd_seed 123</code></pre> <strong>sfb_map</strong>: 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.