Run micca in 6 stepsΒΆ

Open a terminal, download the sample data and prepare the working directory:

wget ftp://ftp.fmach.it/metagenomics/micca/examples/mwanihana.tar.gz
tar -zxvf mwanihana.tar.gz
cd mwanihana

Now we can run micca:

# merge the samples
micca merge -i fastq/*.fastq -o merged.fastq
# trim primers
micca trim -i merged.fastq -o trimmed.fastq -w AGAGTTTGATCMTGGCTCAG -r GTGCCAGCAGCCGCGGTAA -W
# filter low quality reads and truncate at 350 bp
micca filter -i trimmed.fastq -o filtered.fasta -e 0.5 -m 350 -t
# denovo OTU picking protocol
micca otu -i filtered.fasta -o denovo_greedy_otus -d 0.97 -c -t 4
# classify taxonomies using RDP classifier
micca classify -m rdp -i denovo_greedy_otus/otus.fasta -o denovo_greedy_otus/taxa.txt
# export the BIOM file
micca tobiom -i denovo_greedy_otus/otutable.txt -o denovo_greedy_otus/tables.biom -t denovo_greedy_otus/taxa.txt