Requirements

This pipeline is for UGE server with Singularity container environment. Docker also may work, but never tested. If your server use different job scheduler, please edit wrapper scripts (preprocessing_amplicon_all.sh and parse_preprocessed_data.sh).

Run scripts

preprocessing

• Edit file paths in /amplicon-pipeline/script/1-preproccess/preprocessing_amplicon_all.sh for your system.
• Please prepare illumina paired end files on your current directory like this. This pipeline is for ~999 samples.
  • 1_1.fq.gz, 1_2.fq.gz, 2_1.fq.gz, 2_2.fq.gz..., 100_2.fq.gz
• Run sh /path/to/script/preprocessing_amplicon_all.sh 1 100 (100 is just an example.)
• Merge output files for i in `seq -f %03g 1 721`;do cat ${i}/chimera_filtered.fa | sed s/\>/\>${i}_/g >> all_amplicon_seqs.fa; done

OTU clustering, taxonomy mapping (using SILVA database)

• Put all_amplicon_seqs.fa (result of preprocessing) in your current directory.
• Download SILVA database (SILVA_132_SSURef_tax_silva.fasta and taxmap_slv_ssu_ref_132.txt) from https://www.arb-silva.de/download/archive/
• Edit file paths in /amplicon-pipeline/script/2-parse_preprocessed_data/parse_preprocessed_data.sh for your system.
• Run qsub /path/to/script/parse_preprocessed_data.sh.