Analysis scripts GUTS project. Metagenomics shotgun sequencing association with psychiatric patients.
- (for running .smk file) Snakemake v7.12.0, python v3.1
- (for data cleaning) kneaddata v0.10.0 , Bowtie2 v2.2.5, trimmomatic v0.39-2, human ref for mapping: hg37dec_v0.1
- (taxonomic assingment) motus v3.0.3, python v3.7.15 , SAMtools v1.10, BWA v0.7.17
- (SNV calling and intra-species distance ) motus v3.0.3, python v3.7.15 , SAMtools v1.10, BWA v0.7.17
- (GBM quantifiaction) humann v3.1.0, omixer-rpm v1.1, GBMs database (donwloaded 25-01-2023 from http://raeslab.org/software/gbms.html) ###Data analysis
- (for analysis script) R version v4.0.1
- General: tidyverse (v1.3.0), vegan (v2.6-4), ape (v5.4), ggrepl (v0.9.1) , MetBrewer (for color) (v0.2.0)
- Prediction: codacore (0.0.1), tensorflow (2.5.0), pROC (1.17.0.1)
- Batch correction: PLSDAbatch (0.2.3)
- Association: Aldex2 (1.20.0)
- network formatting: igraph (1.2.5)
- (for bulding the network) SparCC (v0.1.0)
- (for analyzing networks) Netshift webapp
###Datasets
- GUTS study participants
- DMP study participants matched to GUTS (age, sex, bmi, socieconomical status) with no dieases
- (validation 1) Zhu et al. schizophrenia pateitns and healthy controls. ENA accesion: PRJEB29127
- (validation 2) DMP sutdy participatns with schizophrenia or bipolar disorder