Run the pipeline on test data:
./fSSU_pipeline_v1.0.sh -t
Run the pipeline on test data with example files:
./fSSU_pipeline_v1.0.sh -1 testdata/mock_R1.fq -2 testdata/mock_R2.fq -b testdata/barcodes.txt -a CLC_assembly_cell -d testdata/mock16S.alignment -c 2
Run pipleline on real data:
./fSSU_pipeline_v1.0.sh -1 R1.fq -2 R2.fq -b barcodes.txt -a CLC_assembly_cell -d SILVA_128_94.alignment -c 2
where:
-h Show this help text
-1 Read1 fastq file
-2 Read2 fastq file
-b Sample barcodes
-a Path to CLC Assembly Cell installation
-d Path to aligned SSU reference database in fasta format with
50000 alignment positions.
-c Number of CPUs to use
-t Flag to run pipeline on test data
Requirements - if your programs are named differently, then change the reference in the respective bash scripts:
mothur (version 1.37.6; https://www.mothur.org/wiki/Download_mothur)
parallel (version 20150422; https://www.gnu.org/software/parallel/)
CLC assembly cell (version 5.0.3; https://www.qiagenbioinformatics.com/products/clc-assembly-cell/)
perl (v5.18.2; https://www.perl.org/get.html)
Experimental pipeline for error-correction of Oxford Nanopore data using molecular tagging