how is this novel? / how compare do existing studies?

• analyze sgc neighborhoods, not assemblies (assemblies will drop too much of the juicy gene bits)

  • if we are working with sgc nbhds, we should probably use protein kmers to get ANI/AAI estimates

• MAGs are composite genomes .. how do we handle?

  • must analyze across samples, not w/in a single sample

• generate a B. sub isolate reference pangenome query
  • Start with a B. sub query
  • Run sourmash prefetch against GTDBrs202
  • Filter to jaccard similarity of >= 0.1
  • Format for genome-grist
  • genome-grist download prefetch matches
  • charcoal decontaminate genomes
  • roary generate reference "pangenome" query
• spacegraphcats query each metagenome CAtlas
• estimate ANI, AAI, Jaccard
• MDS plot
• pangenome statistics of b. sub
  • multifasta annotation of b. sub catlas (genes present)?
  • protein k-mers?
• determine additional content recovered by sgc queries
  • megahit assemble query nbhds
  • map nbhd reads back against query nbhds
  • count number of unmapped reads
  • kmer content analysis in full nbhd vs in assemblies
  • ANI estimation from assemblies

The 605 gut microbiome metagenomes analyzed in this repository were originally analysed in the 2020-ibd repository as a meta-cohort of IBD subtypes (CD, UC, and nonIBD). The download and preprocessing code has been copied over to this workflow, but the pre-processed files have been linked into this repository to save harddisk space. Specifically, k-mer abundance trimmed pre-processed files have been sym linked into outputs/abundtrim, and spacegraphcats metagenome CAtlases have been hard linked into outputs/sgc_genome_queries. The sample metadata file has been copied into this repository from here.

• Genetic Competence Drives Genome Diversity in Bacillus subtilis
• Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains
• A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes

• Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

GTDB extract b sub genomes:

grep -i s__Bacillus gtdb-rs202.taxonomy.v2.csv > bacillus.csv
# then add headers, and...
sourmash sig extract --picklist shewanella.csv:ident:ident /group/ctbrowngrp/gtdb/databases/ctb/gtdb-rs202.genomic.k31.zip -o bacillus.zip

conda env create --name bsub --file environment.yml
conda activate bsub

snakemake -j 16 --use-conda --rerun-incomplete --latency-wait 15 --resources mem_mb=500000 --cluster "sbatch -t 10080 -J bsub -p bmm -n 1 -N 1 -c {threads} --mem={resources.mem_mb}" -k -n