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micca - MICrobial Community Analysis

Stable version: 1.7.2 (2018/08/07)

micca is an open-source, command-line software for the processing of amplicon sequencing data, from raw sequences to OTU tables, taxonomic classification and phylogenetic tree inference. The pipeline can be applied to a range of highly conserved genes/spacers, such as 16S rRNA gene and Internal Transcribed Spacer (ITS).

Main features


Davide Albanese, Paolo Fontana, Carlotta De Filippo, Duccio Cavalieri and Claudio Donati. MICCA: a complete and accurate software for taxonomic profiling of metagenomic data. Scientific Reports 5, Article number: 9743 (2015), doi:10.1038/srep09743, Link. Dataset download:



Dereplication, denoising and chimera filtering in one step, using 4 threads:

$ micca otu -m denovo_unoise -i input.fasta -o outdir -t 4 -c

Discard reads with expected error rate >0.5% and shorter than 300 bp:

$ micca filter -i input.fastq -o output.fasta -e 0.5 -m 300

Third-party software

micca wraps third-party software packages and these should be cited if they are used: