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ibd

Analysis of publicly available metagenomic sequencing data from humans with IBD.

Purpose

Implements analyses written up here: https://dib-lab.github.io/2021-paper-ibd/

Getting started with this repository

The bulk of this pipeline is executed with the Snakefile.

This repository uses conda to manage software installations. You can find operating system-specific instructions for installing miniconda here.

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

An example command to run on cluster with slurm is included below (dry run):

snakemake -j 33 --use-conda --rerun-incomplete --latency-wait 15 --resources mem_mb=400000 --cluster "sbatch -t 1440 -J ibdsmk -p bmm -n 1 -N 1 -c {threads} --mem={resources.mem_mb}" -k -n

Improvements I would make if I were to do it all again

A list, in no particular order. Some are trivial, some are a big deal

  • Make the preprocessing steps host remove with bbduk -> quality trim with fastp -> kmer trim with khmer (see https://github.com/dib-lab/distillerycats/blob/main/distillerycats/Snakefile)
  • Update from sourmash compute to sourmash sketch
  • Make spacegraphcats rules proper snakemake checkpoints
  • Upgrade to GTDB rs207 (or whatever GTDB is most current)
  • Do all interpretation analysis in jupyter notebooks (even for R code) so figures are inline with code and easier to keep track of (note I converted most analyses over to notebooks).