Skip to main content

micca - MICrobial Community Analysis

Project description

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) and 28S rRNA.

For more information, visit

Key features

  • supports single-end (Roche 454, Illumina MiSeq/HiSeq ,Ion Torren) as well overlapping paired-end reads (Illumina MiSeq/HiSeq);
  • multithread de novo greedy clustering as well closed-reference and open-reference OTU picking protocols are available;
  • state-of-the-art taxonomic classification algorithms are available (RDP and consensus-based classifier);
  • fast (multithread) and and memory efficient implementation of the NAST multiple sequence alignment (MSA);
  • filter low quality sequences according to the maximum allowed expected error (EE) rate %;
  • simple, easy to use.

Citing micca

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.

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

  • VSEARCH 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

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for micca, version 1.2.2
Filename, size File type Python version Upload date Hashes
Filename, size micca-1.2.2.tar.gz (1.9 MB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page