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README.rst

micca - MICrobial Community Analysis

https://travis-ci.org/compmetagen/micca.svg?branch=master

micca (MICrobial Community Analysis) is a software pipeline for the processing of amplicon sequencing data, from raw sequences to OTU tables, taxonomy classification and phylogenetic tree inference. The pipeline can be applied to a range of highly conserved genes/spacers, such as 16S rRNA gene, Internal Transcribed Spacer (ITS) 18S and 28S rRNA. micca is an open-source, GPLv3-licensed software.

Key features:

  • supports single-end (Roche 454, Illumina MiSeq/HiSeq ,Ion Torrent) and overlapping paired-end reads (Illumina MiSeq/HiSeq);
  • multithread de novo greedy, closed-reference, open-reference and swarm OTU picking protocols;
  • denoising of Illumina reads;
  • state-of-the-art taxonomic classification algorithms (RDP and consensus-based classifier);
  • fast and and memory efficient NAST multiple sequence alignment (MSA);
  • filters low quality sequences according to the maximum allowed expected error (EE) rate %;
  • runs on Linux, Mac OS X and MS Windows (through Docker containers)
  • simple, easy to use.

Docker images are available (compmetagen/micca) starting from version 1.2.2, see the documentation (>=1.3.0) to learn how to use them. Docker hub page.

How to cite: 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/.

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