Microbial Identification and Characterization through Reads Analysis


MICRA is a pipeline for the Microbial Identification and Characterization through Reads Analysis. Contrary to the current approaches often based on de novo assembly and contig annotation, MICRA is based on read mapping and comparative genomics, exploiting the growing knowledge in databases. Due to its concept, MICRA is fast, requiring only few minutes to run.
MICRA is an entirely automatic pipeline, offering an easy-to-use web interface and readable results. The only required parameters are the reads in FASTQ format and the sequencing technology. For more specialized task, the MICRA interface gives access to a lot of parameters allowing a customized analysis.
The results produced are human readable and reproducible. MICRA was evaluated on several studies (see the associated publication), all the results (available here) showing that MICRA is fast, efficient and provides new insight for fundamental and clinical microbiology.
In addition to the reads analysis pipeline, an other tool called MICRA Comparison is available to easily compare several result files generated with MICRA. This module allows the user to compare the annotations and/or the variant calls for several samples. A Venn diagram is produced to easily compare the samples; the text files corresponding to the different parts of the Venn diagram are also available.

Quick Links:

To access the MICRA pipeline use the MICRA web-interface.
To compare several result files generated with MICRA use the MICRA Comparison web-interface.
For more details about how to use MICRA, please see the detailed user guide and the MICRA FAQ.

Description of the MICRA pipeline

MICRA is divided into 4 main parts.

  1. The pre-processing part, which is optional, allows read quality check and trimming.
  2. The sequence identification part aims to obtain the reference sequences used in the core part of MICRA.
  3. The core part identifies the closest reference genome and the plamids, produces the sequences and annotations from iterative mapping and performs de novo assembly with the remaining unmapped reads to generate additionnal annotations.
  4. The post-analysis part is able to predict the antibiotic susceptibility and resistance profile from the MICRA results and to compare several samples with the MICRA comparison tool.

For more details about the MICRA pipeline, please see the associated publication.

External tools and databases used in MICRA

MICRA uses several external tools and databases:

The MICRA Comparison module uses R with the VennDiagram package.


If you make use of the MICRA pipeline, please cite us:
Caboche et al., MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data, Genome Biol. 2017;18(1):233. [publication]