Pipeline example: HMP 454 16S V5-V3
OTU / denoising
Example pipelines with test
This example shows a typical analysis
pipeline for 454. Data is
You need to set
the environment variable $usearch to the name (or path) for your
usearch binary file. The bash script
assumes that the FASTQ files, barcodes and sintax reference database are
stored in a directory called ../data. Output is written to a directory
called ../out which is deleted and re-build. I suggest making a project
directory, say ex_hmp, with sub-directories named data and scripts. Put the
ex_hmp.bash script in the scripts sub-directory and execute it from there.
Download commands and data
Reads and barcodes: right-click on
and click Save As. Use tar -zxvf *.tar.gz to extract.
reference database: right-click on
rdp_16s_v16.fa.gz and click Save As. Use gunzip
Bash script: select all text below (ctrl+A) and
copy/paste into a text editor, or right-click on
ex_hmp.bash and click Save As.