Requirements

The following programs should be installed with commands accessible from the user's PATH, before trying to run any of the scripts included in this repository.

Both pipelines

• FastQC (optional): http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
• PEAR: http://sco.h-its.org/exelixis/web/software/pear/doc.html

Metagenomics

• Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
• Human pre-indexed database: ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes/hg19.zip
• DIAMOND (> v.0.7.0): http://ab.inf.uni-tuebingen.de/software/diamond/
• MetaPhlAn2: https://bitbucket.org/biobakery/metaphlan2
• HUMAnN: http://huttenhower.sph.harvard.edu/humann

16S

• FASTX toolkit (v0.0.14): http://hannonlab.cshl.edu/fastx_toolkit/download.html
• BBMap: http://sourceforge.net/projects/bbmap
• VSEARCH: https://github.com/torognes/vsearch
• QIIME: http://qiime.org
• SortMeRNA: http://bioinfo.lifl.fr/RNA/sortmerna/
• SUMACLUST: http://metabarcoding.org/sumatra
• PICRUSt: http://picrust.github.io/picrust/

Visualization

• STAMP: http://kiwi.cs.dal.ca/Software/STAMP

Databases (dropbox download links)

• 16S chimera checking: Bacteria_RDP_trainset15_092015.fa (17 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] (https://www.dropbox.com/s/p4wnjyvatdobq5h/Eukaryota_SILVA_123_SSURef_Nr99_tax_silva_U-replaced.fasta?dl=1) (117 MB). This DB was taken from SILVA and was parsed to include only eukaryotes and all Us were converted to Ts.

• Eukaryotic OTU-picking files:

  • [gb203_pr2_all_10_28_99p_tax_Xs-fixed_poly-fixed.txt] (https://www.dropbox.com/s/bvot58v47rfc6a2/gb203_pr2_all_10_28_99p_tax_Xs-fixed_poly-fixed.txt?dl=1) (9MB)
  • gb203_pr2_all_10_28_99p_clean.fasta (98 MB)
  • Silva_119_rep_set90_aligned_18S.fna (112 MB)

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

• To use "run_pre_humann.pl" you will need to use a database of KEGG orthologs.

Perl modules

File::Basename Getopt::Long List::Util Parallel::ForkManager Pod::Usage