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Application data

Created by Bastien Chevreux
Biological application domain(s) Sequence assembly (de novo assembly), SNP detection, RNA-Seq alignment
Principal bioinformatics method(s) Local sequence alignment, graph reduction, learning algorithm, Sequence assembly, Read mapping, k-mer counting
Technology Sanger, Illumina, 454, PacBio, Ion Torrent
Maintained? Yes
Input format(s) FASTA, FASTQ, CAF, GenBank, GBFF, EXP, PHD, SCF, XML traceinfo
Output format(s) ACE, CAF, EXP, HTML, TXT, TCS
Programming language(s) C++
Licence GPL
Operating system(s) Linux, Mac OS X, UNIX

Summary: MIRA 3 - Whole Genome Shotgun and EST Sequence Assembler


Hybrid de-novo assemblies with Sanger, 454 and Illumina / Solexa

MIRA 3 is able to perform true hybrid de-novo assemblies using reads gathered through Sanger, 454 or Solexa sequencing technologies. That is, it assembles reads instead of a mix of (eventually shredded) shredded consensus sequence and reads. This works for Sanger and 454, but also with Sanger/Solexa or 454/Solexa or Sanger/454/Solexa. The length of the Solexa sequences is not restricted, they can be 36mers to 150mers or more.

Automatic sequence editors

MIRA contains integrated editors for Sanger and 454 sequences which iteratively remove many sequencing errors from the assembly project and improve the overal alignment quality.

SNP and mutations discovery for de-novo or mapping assemblies

MIRA 3 can also be used for mapping assemblies and automatic tagging of difference site (SNPs, insertions or deletions) of mutant strains against a reference sequence.

For organisms without exon/intron gene structure (bacteria, viruses etc.) and where annotated files in GenBank format are available, MIRA can generate tables which are ready to use for biologists as they show exactly which genes are hit and give a first estimate whether the function of the protein is attained by the change.



  1. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, Suhai S.. 2004. Genome Research

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