This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
Latest Version Dependencies status unknown Test status unknown Test coverage unknown
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.

micca is an open-source, GPLv3-licensed software.

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
  • closed-reference, open-reference and swarm OTU picking protocols;
  • 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);
  • 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

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:.

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. Dataset download.

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

  • VSEARCH (https://github.com/torognes/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
  • swarm (10.7717/peerj.593, doi: 10.7717/peerj.1420) used in the otu command
Release History

Release History

1.5.0

This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

1.4.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

1.3.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

1.2.2

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

1.2.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

1.1.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

1.0.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
micca-1.5.0.tar.gz (2.0 MB) Copy SHA256 Checksum SHA256 Source Jun 14, 2016

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS HPE HPE Development Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting