micca 1.7.2

Description:

micca 1.7.2

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.

Homepage
Documentation (latest)
Issues
Github page

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