FIGARO will quickly analyze error rates in a directory of FASTQ files to determine optimal trimming parameters for high-resolution targeted microbiome sequencing pipelines, such as those utilizing DADA2 and Deblur. The mission of this application is identical to the ZymoBIOMICS mission: increasing the reproducibility and standardization of microbiome analysis.
See versions that are available:
$ module avail figaro
Load one version into your environment and run it:
$ module load figaro/git-337aa9 $ figaro -h
Notes from the sysadmin during installation.
$ cd /tmp $ git clone https://github.com/Zymo-Research/figaro.git $ module load python/3.8 $ sudo mkdir -p /export/apps/figaro/git-337aa9 $ sudo chown aorth /export/apps/figaro/git-337aa9 $ python3 -m venv /export/apps/figaro/git-337aa9/venv $ source /export/apps/figaro/git-337aa9/venv/bin/activate $ pip install --upgrade pip setuptools wheel $ pip install -r requirements.txt $ python setup.py install $ sudo chown -R root:root /export/apps/figaro/git-337aa9