Anacapa is a toolkit designed to construct reference databases and assign taxonomy, from eDNA sequences.
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mkdir ~/anacapa/crux_db/EMBL cd ~/anacapa/crux_db/EMBL wget https://www.funet.fi/pub/sci/molbio/embl_release/std/rel_std_mam_01_r143.dat.gz wget https://www.funet.fi/pub/sci/molbio/embl_release/std/rel_std_mam_02_r143.dat.gz gzip -d rel_std_mam_01_r143.dat.gz gzip -d rel_std_mam_02_r143.dat.gz |
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#alternatively: download all EMBL files wget https://www.funet.fi/pub/sci/molbio/embl_release/std/rel* #uncompress all downloaded files for i in `ls rel*`; do echo $i; gzip -d $i; done |
Again, in this guide we’re just looking at mammal sequences. If you’re looking at another taxonomic group, you’ll need to download the appropriate databases. below are the codes for the available EMBL taxonomic groups.
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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.
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