microbiome_shotgun_pipeline

TODO

anvi'o test

• read http://merenlab.org/2016/06/22/anvio-tutorial-v2/
• see http://merenlab.org/2018/07/09/anvio-snakemake-workflows/
• gene call: import prodigal gene call
• kaiju annotation for gene call

metagenome assembly and binning

• CAT/BAT taxonomy of contigs
• see http://merenlab.org/tutorials/infant-gut/#chapter-ii-incorporating-automatic-binning-results
• binning metabat
• binning CONCOCT (embedded in anvio)
• binning groopM
• binning MyCC
• binnin BinSanity
• bin refinment (https://github.com/cmks/DAS_Tool)
• dereplication (https://github.com/MrOlm/drep)
• show assembly contiguity on GC vs Coverage plot

relative abundance

• mOTUs
• visualization

AMR, virulence and mobility gene identification

• VFDB + SwissProt toxins/virulence factors: extract data from fasta and sqlite database
• COG X (Mobilome: prophages, transposons): ftp://ftp.ncbi.nih.gov/pub/COG/COG2014/data/cognames2003-2014.tab (119 entries)
• UNIPROT Transposable element [KW-0814] (taxonomy:"Bacteria [2]" keyword:"Transposable element [KW-0814]" AND reviewed:yes) (433 entries)
• CARD (protein)
  • remove variant model, resistance by absence, molecular bypass, ...
• cluster at 95% identity
• mmseqs2 indexing
• mmseqs2 search
• calculate RPKM (reads per million per sequence length)
• heatmap abundance of VF