microbiome_strain_species_nanopore_quantification_tarfiles

a.  Code repository is  https://github.com/cjwoodruff50/Nanopore_WEHI_cjw  

     A description of the code pipeline is provided there. Item b. below describes key data files.

 

b.  1. Input for database generation is in   .../papercheck/workDB1, including the 

       sub-directories 16S and 23S which contain the fasta files of each strains' rRNA 

       genes. The following tarred files hold the relevant data:-

           workDB1_16S_fasta_03022024.tar

           workDB1_23S_fasta_03022024.tar

           workDB1_16S_23S_blastn_databases.tar

    2. Input for dataset generation is the split_zymo_hmw_r104_* files  (aa to cx)

       These have been tarred into 

           split_zymo_hmw_r104_aa_cx.tar

           

       Processing of these files by extract_Seraika_16S23S_v10.R  generates the primary 

       16s and 23S datasets.

       

       Separately for both 16S and 23S 

          

    3. Input for RAD denoising is 10 fastq files. The primary datasets are in 

       .../papercheck/in   while the sub-sampled datasets are in .../papercheck

          amplicon_16S_RADfastqinput_subsampledDatasets_05022024.tar    and

          amplicon_23S_RADfastqinput_subsampledDatasets_05022024.tar

       hold the sub-sampled datasets' fastq files.

   

    4. Input for ASV alignments, and profiling based on these, RAD outputs and the 

       reference databases.  These are held in 

          amplicon_16S_RADfastqoutput_05022024.tar

          amplicon_23S_RADfastqoutput_05022024.tar

          denoised_amplicon_D6322_16S23S_05022024_10datasets_ASVs_fasta.tar

       The reference databases (see i. above)  are also required, of course.

       

    Necessary data for running the denoising and profiling consists of 

           

       i.    workDB1_16S_23S_blastn_databases.tar

      ii.    amplicon_D6322_16S_trimmed_05022024.fastq

     iii.    amplicon_D6322_23S_trimmed_05022024.fastq

           

      iv.    amplicon_16S_RADfastqinput_subsampledDatasets_05022024.tar

       v.    amplicon_23S_RADfastqinput_subsampledDatasets_05022024.tar

           

      vi.    denoised_amplicon_D6322_16S23S_05022024_10datasets_ASVs_fasta.tar

     vii.    amplicon_16S_RADfastqoutput_05022024.tar

    viii.    amplicon_23S_RADfastqoutput_05022024.tar

      ix.    RAD_amplicon_16S23S_05022024_10datasets_text_output_06022024.tar

    

    Items i. to iii. allow RAD denoising of the primary 16S and 23S datasets.

    Items iv. and v., together with item i. allow RAD denoising of the sub-sampled 

             datasets

    Items vi., vii., viii. and ix. allow identification and quantification of the sample 

             microbiota for all datasets.