This repository contains code used in the multiomic analyses of faecal microbiota from four families with several cases of T1DM ( MuSt ).

You can find the different scripts behind the links next to the bullet points below. The links in the sub-headings below lead to descriptions of the workflows which connect the different scripts.

to build a search data base for proteomics from predicted proteins and their variants:

• rename4proteomics.pl
• trypsinStartEndProdigal.pl (corrected version)
• variant_annotateRepairedTabProdigal.pl (corrected version)
• variants_annotateTab4StatsProdigal.pl (corrected version)
• trypsinStartEnd.pl (old version)
• variant_annotateRepairedTab.pl (old version)
• variant_annotateRepairedTabProdigalStillWrong.pl (version to keep workflow)
• variants_annotateTab4Stats.pl (old version)
• variants_locateType.pl

to parse functional annotations of gene predictions (some including coverage):

• 150310_MUST_hmmBestAll.py
• 150705_MUST_hmmParse.py
• 150705_MUST_hmmParsePfam.py
• consolidate_hmmscan_results.pl
• consolidate_hmmscan_results_justKEGG.pl
• 150705_MUST_keggParseNW.py
• ko2des_clean.txt - pretty big text file
• calculateCoverageAndGaps2.pl
• 150322_bestHmmReadParse.py
• 150415_bestHmmAveCovParse.py
• 150630_keggReadParse.py

to annotate phylogenetic marker genes with the taxonomy of the best hit from the mOTU database:

• fastaExtractWithCoordBase1.pl
• getValidGenes1.R
• getValidGenes2new.R
• getHitPhylogenyNew.R

to parse taxonomy of MG-RAST annotations of genes:

• parse_taxbrowser_MGRAST.py
• MGRASTgeneLevelTax.R

to automatically cluster contigs based on nucleotide signature (BH-SNE maps), DNA coverage and essential genes:

• autoCluster.R
• fastaExtractCutRibosomal1000.pl
• makeWSvarAnnoCorrect.R

to gather contig clusters by related phylogenetic marker genes in a phylogenetic tree:

• 150819_MUST_tree.R
• 150816_getPhyloMarkers.R

to reconstruct a metabolic network from KOs and analyse it:

• 140630_MUST_NW.R
• the above script needs file 150705_KOs_in_NW.tsv
• runHeinz.sh
• plotModules_omicLevels.R

to feed a mongo database with all the data from MuSt and retrieve some of the data:

• 150928_mongifyMust.py
• 151020_funOIMongoWS.R
• 150928_MUST_relatedClusterWSFromMongo.R
• eukaryoticGenesMongo.R
• virusGenesMongo.R
• getNWexprMongoAllSamples.R