Convert DADA2 Seqtabs to QIIME files
usage: dada2_to_qiime.py [-h] -i INPUT [-t THREADS] [-p PREFIX]
Convert a dada2 seqtab to qiime formatted goodies
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
The input file
-t THREADS, --threads THREADS
The number of threads to use for QIIME functions
-p PREFIX, --prefix PREFIX
The prefix for each unique sequence variant i.e SV1
After creating your bimeric filtered seqtab in DADA2, write it out to a CSV
seqtab.nochim <- removeBimeraDenovo(seqtab, verbose=TRUE, multithread=TRUE)
write.csv(seqtab.nochim, file = "seqtab.nochim.csv")
Next run the dada2_to_qiime.py script
dada2_to_qiime.py -i seqtab.nochim.csv
This will create:
- seqtab.nochim.otutable
- seqtab.nochim.repset
- dada_to_qiime.sh
seqtab.nochim.otutable
A transposed version of the seqtab.nochim.csv with each fill length sequence variant replaced with a simple numerical notation, i.e. SV1
seqtab.nochim.repset
A mapping between the numerical notations and the actual sequence variants
dada_to_qiime.sh
A shell script that will
- Build a tree
- Assign taxonomy
- Create a biom
- Create a new level of taxa for looking at sequence variants
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