Anacapa is a toolkit designed to construct reference databases and assign taxonomy, from eDNA sequences.
...
Run the obiconvert command from the anacapa Singularity image.
Important: You need to change every instance of /home/your_home_directory in the below command to your actual home directory (this is because obiconvert requires absolute paths). To find your home directory path, type cd ~ and then pwd. Use the path that this displays to replace the /home/your_home_directory.
...
-t Illumina Platform: HiSeq (2 x 150) or MiSeq (>= 2 x 250)
| Code Block |
|---|
singularity exec /home/whatmorp/nextflow/pia_eDNAFlow/Anacapa/anacapa-1.5.0.img /bin/bash /home/whatmorp/nextflow/pia_eDNAFlow/Anacapa/anacapa/Anacapa_db/anacapa_QC_dada2.sh -i /home/whatmorp/nextflow/pia_eDNAFlow/fastq -o /home/whatmorp/nextflow/pia_eDNAFlow/Anacapa/16Smam_anacapa_output -d /home/whatmorp/nextflow/pia_eDNAFlow/Anacapa/anacapa/Anacapa_db -a nextera -t MiSeq -g -l |
Cleanup
Running the anacapa workflow involves downloading and generating various large databases. These will just take up space on the HPC unless removed.
...