Mock community reference for seq.error

[amwalkero0o]

Hello there,

The reference fasta file for my mock community from zymoresearch is formatted such that each microbe in the community has it’s own fasta file versus having one fasta file for all taxa. How do I use this format in the seq.error command?

The fasta files I have look like this:
Bacillus_subtilis_16S_170923.fasta
Listeria_monocytogenes_16S_170923.fasta
Cryptococcus_neoformans_18S_170924.fasta Pseudomonas_aeruginosa_16S_170923.fasta
Cryptococcus_neoformans_Mitochondria_ssrRNA.fasta Saccharomyces_cerevisiae_18S_170924.fasta
Enterococcus_faecalis_16S_170923.fasta Saccharomyces_cerevisiae_mitochondria_ssrRNA.fasta
Escherichia_coli_16S_170923.fasta
Salmonella_enterica_16S_170923.fasta
Lactobacillus_fermentum_16S_170924.fasta
Staphylococcus_aureus_16S_170923.fasta

[amwalkero0o]

I’ve found the answer here. Basically you want to get rid of mitochondrial fasta files and concatenate the bacterial fasta files:

wget -N https://s3.amazonaws.com/zymo-files/BioPool/ZymoBIOMICS.STD.refseq.v2.zip
unzip ZymoBIOMICS.STD.refseq.v2.zip
cd ZymoBIOMICS.STD.refseq.v2/ssrRNAs
rm *_Mitochondria_ssrRNA.fasta
cat *.fasta > zymo_temp.fasta
sed '0,/Salmonella_enterica_16S_5/{s/Salmonella_enterica_16S_5/Salmonella_enterica_16S_7/}' zymo_temp.fasta > zymo.fasta 

seq.error(fasta=testy.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta, count=testy.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table, reference=zymo.fasta , aligned=F)