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).

• Documentation (1.6.1-latest)
• Old documentation (0.1-1.6.0))
• Issues
• Users forum
• Github page

Main features

• single-end (454, Illumina MiSeq/HiSeq) and overlapping paired-end reads;
• state-of-the-art OTU picking protocols;
• denoising of Illumina reads;
• taxonomic classification (RDP and consensus-based classifier);
• fast and memory efficient NAST multiple sequence alignment (MSA);
• maximum allowed expected error (EE) rate % filtering;
• runs on Linux, Mac OS X and MS Windows (through Docker containers);
• simple, easy to use.

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Citing

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: ftp://ftp.fmach.it/metagenomics/micca/scirep/.

Install

• Using PIP $ pip install micca
• Docker images are availablesince version 1.2.2 $ docker pull compmetagen/micca
• From sources $ python setup.py install

Examples

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:

• VSEARCH (doi: 10.7717/peerj.2584) used in classify, filter, mergepairs, otu and msa commands
• MUSCLE (doi: 10.1093/nar/gkh340) used in msa and tree commands
• FastTree (doi: 10.1371/journal.pone.0009490) used in the tree command
• Cutadapt (doi: 10.14806/ej.17.1.200) used in the trim command
• RDP classifier (doi: 10.1128/AEM.00062-07) used in the classify command
• swarm (doi: 10.7717/peerj.1420) used in the otu command