Past SOP databases - merckey/microbiome_helper GitHub Wiki

Note these requirements are for the original SOPs are no longer needed.

Databases (dropbox download links)

• 16S chimera checking: RDP_trainset16_022016.fa (20 MB). This DB was originally from the Ribosome Database Project (RDP) and was parsed to include only bacteria.

• 18S chimera checking: Eukaryota_SILVA_123_SSURef_Nr99_tax_silva_U-replaced.fa (117 MB). This DB was taken from SILVA and was parsed to include only eukaryotes and all Us were converted to Ts.

• ITS2 chimera checking: UNITE_uchime_ITS2only_01.01.2016.fasta (8.6 MB) taken from UNITE database.

• Eukaryotic OTU-picking files (from the PR2 database):

  • gb203_pr2_all_10_28_99p_tax_Xs-fixed_poly-fixed.txt (9 MB)
  • gb203_pr2_all_10_28_99p_clean.fasta (98 MB)
  • 90_Silva_111_rep_set_euk_aligned.filter.fasta (95 MB)

• ITS2 OTU-picking files (taken from UNITE database):

  • UNITE_sh_refs_qiime_ver7_dynamic_20.11.2016.fasta (16.9 MB).
  • UNITE_sh_refs_qiime_ver7_dynamic_20.11.2016.goodASCII.txt (4.2 MB) - we converted all non-ASCII characters to ASCII format.

• To use "run_contaminant_filter.pl" you will need to download the appropriate Bowtie2 index.