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Home modified by Bastien Chevreux

Bastien Chevreux — Tue, 07 Jan 2025 20:56:29 -0000

--- v4
+++ v5
@@ -1,6 +1,7 @@
 **MIRA** is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads). It can be seen as a Swiss army knife of sequence assembly developed and used in the past 16 years to get assembly jobs done efficiently - and especially accurately. That is, without actually putting too much manual work into finishing the assembly. 

-The latest stable version is [MIRA 4.0](http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/)
+The previous version of [MIRA 4.0](http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/) on SourceForge.
+The latest stable version is [MIRA 5](https://github.com/DrMicrobit/mira/releases) on GitHub!

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@@ -9,13 +10,6 @@
 [TOC]

 ---------
-
-## Quicklinks ##
-* Visit the [project page](http://sourceforge.net/projects/mira-assembler/) on SourceForge
-* Download the [latest release](http://sourceforge.net/projects/mira-assembler/files/) either as source or as binary for Linux or OSX
-* See some interesting features of MIRA 4 [explained in action](http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#chap_intro_specialfeatures)
-* Found a bug or have a feature request? [File it here](http://sourceforge.net/apps/trac/mira-assembler/) and also send a quick mail to the MIRA talk mailing list
-* Need help? Want to discuss something with other users? There are [mailing lists](http://chevreux.org/mira_mailinglists.html) for MIRA

 ## Documentation ##
 The most up-to-date documentation is also always available in the binary distribution packages.

Home modified by Bastien Chevreux

Bastien Chevreux — Sun, 02 Feb 2014 13:39:38 -0000

--- v3
+++ v4
@@ -34,7 +34,7 @@

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

-MIRA 4 is able to perform true hybrid de-novo assemblies using reads gathered through Sanger, 454, Solexa, IonTorrent or PacBio sequencing technologies. That is, it assembles reads instead of a mix of (eventually shredded) consensus sequence and reads. See an example on how it looks like for Sanger and 454 in the documentation introduction, but it also works with any other combination of sequencing technologies. Only restriction at the moment: reads must be <= 25 kilobases and for PacBio, MIRA must get CCS reads or error-corrected CLR data.
+MIRA 4 is able to perform true hybrid de-novo assemblies using reads gathered through Sanger, 454, Solexa, IonTorrent or PacBio sequencing technologies. That is, it assembles reads instead of a mix of (eventually shredded) consensus sequence and reads. See an example on how it looks like for Sanger and 454 in the documentation introduction, but it also works with any other combination of sequencing technologies. Only restriction at the moment: reads must be <= 32 kilobases and for PacBio, MIRA must get CCS reads or error-corrected CLR data.

 The combination currently preferred by the author is a mix of de-novo error-corrected PacBio reads and Illumina mapping assemblies: PacBio to get long contigs built, Illumina to get rid of the indels which even Quiver (PacBio software) cannot get rid of. Here's the recipe I use for sequencing a bacterium or lower eukaryote de-novo and almost perfectly for comparatively little money:

Home modified by Bastien Chevreux

Bastien Chevreux — Sun, 02 Feb 2014 12:46:20 -0000

--- v2
+++ v3
@@ -1,8 +1,6 @@
-MIRA - Sequence assembler and mapper for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina, IonTorrent and pre-corrected PacBio data.
+**MIRA** is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads). It can be seen as a Swiss army knife of sequence assembly developed and used in the past 16 years to get assembly jobs done efficiently - and especially accurately. That is, without actually putting too much manual work into finishing the assembly.

-**MIRA** is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads). It can be seen as a Swiss army knife of sequence assembly developed and used in the past 12 years to get assembly jobs done efficiently - and especially accurately. That is, without actually putting too much manual work into finishing the assembly. 
-
-The latest stable version is [MIRA 4.0rc1](http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/)
+The latest stable version is [MIRA 4.0](http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/)

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@@ -38,19 +36,19 @@

 MIRA 4 is able to perform true hybrid de-novo assemblies using reads gathered through Sanger, 454, Solexa, IonTorrent or PacBio sequencing technologies. That is, it assembles reads instead of a mix of (eventually shredded) consensus sequence and reads. See an example on how it looks like for Sanger and 454 in the documentation introduction, but it also works with any other combination of sequencing technologies. Only restriction at the moment: reads must be <= 25 kilobases and for PacBio, MIRA must get CCS reads or error-corrected CLR data.

-An often used combination of current sequencing technologies is a mix of de-novo 454 assembly and Solexa mapping assemblies: 454 to get long contigs built, Solexa to get rid of the pesky 454 homopolymer problems. Here's the recipe I use for sequencing a bacterium de-novo and almost perfectly for comparatively little money:
+The combination currently preferred by the author is a mix of de-novo error-corrected PacBio reads and Illumina mapping assemblies: PacBio to get long contigs built, Illumina to get rid of the indels which even Quiver (PacBio software) cannot get rid of. Here's the recipe I use for sequencing a bacterium or lower eukaryote de-novo and almost perfectly for comparatively little money:

-1. get your DNA sequenced at ~30x coverage with 454 Titanium
-* get the very same DNA sequenced at ~30-40x coverage with Illumina (100 or more base pairs)
-* put the sequences of 454 and Solexa (and Sanger, if you have) into MIRA
-* wait over night for the result
+1. get your DNA sequenced at ~100x polymerase read coverage with PacBio
+* get the very same DNA sequenced at ~30-100x coverage with Illumina (100 or more base pairs)
+* get the error corrected sequences from the HGAP pipeline and assemble them with MIRA
+* map Illumina data to the assembly above with MIRA
 * add half a day or so for prettifying the resulting assembly and check remaining uncertainties (if you really want to) with gap4

 Granted, there may be a few more steps ... but that's basically it.

 ## 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.
+MIRA contains integrated editors for all sequence technologies which iteratively remove many sequencing errors from the assembly project and improve the overal alignment quality.

 ## SNP and mutations discovery for mapping assemblies ##

Home modified by Bastien Chevreux

Bastien Chevreux — Sat, 17 Aug 2013 15:46:25 -0000

--- v1
+++ v2
@@ -1,8 +1,78 @@
-Welcome to your wiki!
+MIRA - Sequence assembler and mapper for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina, IonTorrent and pre-corrected PacBio data.

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
+**MIRA** is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads). It can be seen as a Swiss army knife of sequence assembly developed and used in the past 12 years to get assembly jobs done efficiently - and especially accurately. That is, without actually putting too much manual work into finishing the assembly. 

-The wiki uses [Markdown](/p/mira-assembler/wiki/markdown_syntax/) syntax.
+The latest stable version is [MIRA 4.0rc1](http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/)

+----------
+
+**Table of contents**
+
+[TOC]
+
+---------
+
+## Quicklinks ##
+* Visit the [project page](http://sourceforge.net/projects/mira-assembler/) on SourceForge
+* Download the [latest release](http://sourceforge.net/projects/mira-assembler/files/) either as source or as binary for Linux or OSX
+* See some interesting features of MIRA 4 [explained in action](http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#chap_intro_specialfeatures)
+* Found a bug or have a feature request? [File it here](http://sourceforge.net/apps/trac/mira-assembler/) and also send a quick mail to the MIRA talk mailing list
+* Need help? Want to discuss something with other users? There are [mailing lists](http://chevreux.org/mira_mailinglists.html) for MIRA
+
+## Documentation ##
+The most up-to-date documentation is also always available in the binary distribution packages.
+
+* Whole documentation, stable version as [HTML, one file](http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html) (800 KiB + 3 MiB images)
+* Whole documentation, stable version: [PDF](http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.pdf) (3.5 MiB)
+
+
+Scaffolding:
+* [Scaffolding with Bambus](http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf) Instructions for scaffolding MIRA contigs & paired-end data with BAMBUS. Written by Gregory Harhay, USDA.
+
+## Short history ##
+MIRA started in 1997 as a PhD project at the German Cancer Research Centre in Heidelberg (Deutsches Krebsforschungszentrum Heidelberg). Binaries were always distributed publicly and over time, other labs and sequencing providers have found MIRA useful for assembly of extremely 'unfriendly' projects containing lots of repetitive sequences (as always, your mileage may vary).
+
+In 2007 I (Bastien Chevreux) asked the DKFZ for the permission to put MIRA under an open source license ... and got it.
+
+## Hybrid de-novo assemblies with Sanger, 454, Illumina / Solexa, IonTorrent and PacBio ##
+
+MIRA 4 is able to perform true hybrid de-novo assemblies using reads gathered through Sanger, 454, Solexa, IonTorrent or PacBio sequencing technologies. That is, it assembles reads instead of a mix of (eventually shredded) consensus sequence and reads. See an example on how it looks like for Sanger and 454 in the documentation introduction, but it also works with any other combination of sequencing technologies. Only restriction at the moment: reads must be <= 25 kilobases and for PacBio, MIRA must get CCS reads or error-corrected CLR data.
+
+An often used combination of current sequencing technologies is a mix of de-novo 454 assembly and Solexa mapping assemblies: 454 to get long contigs built, Solexa to get rid of the pesky 454 homopolymer problems. Here's the recipe I use for sequencing a bacterium de-novo and almost perfectly for comparatively little money:
+
+1. get your DNA sequenced at ~30x coverage with 454 Titanium
+* get the very same DNA sequenced at ~30-40x coverage with Illumina (100 or more base pairs)
+* put the sequences of 454 and Solexa (and Sanger, if you have) into MIRA
+* wait over night for the result
+* add half a day or so for prettifying the resulting assembly and check remaining uncertainties (if you really want to) with gap4
+
+Granted, there may be a few more steps ... but that's basically it.
+
+## 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 mapping assemblies ##
+
+MIRA 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 where annotated files in GFF3 format are available (or for GenBank files without intron/exon structures), 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.
+
+
+## Publications ##
+### Papers ###
+* Chevreux et al. (1999) [Genome Sequence Assembly Using Trace Signals and Additional Sequence Information](http://www.bioinfo.de/isb/gcb99/talks/chevreux/) Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. There are also slides for the talk held at the conference, get them [here](http://chevreux.org/dkfzold/gcb99/bachvortrag_gcb99.ppt).
+* Chevreux et al. (2004) [Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs](http://genome.cshlp.org/content/14/6/1147.full) Genome Research 2004. 14:1147-1159.
+
+### Posters ###
+* Chevreux et al. (1998) [Computer assisted editing of genomic sequences](http://chevreux.org/dkfzold/publ/poster-gp98-gcb98/poster.html) poster at the "Genome and Proteomics 98" in Heidelberg and the "German Conference on Bioinformatics" GCB 98 in Cologne (english) 
+* Chevreux et al. (1999) [MIRA & EdIt](http://chevreux.org/dkfzold/publ/poster-ismb99-gcb99/ismb99.html) poster presented at the ISMB 99 conference in Heidelberg and the "German Conference on Bioinformatics" GCB 99 in Hannover
+
+## Sponsors ##
+* 1997 to 2000: Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie by grant number 01 KW 9611
+
+
+
+[[project_screenshots]]
 [[members limit=20]]
 [[download_button]]

Home modified by Bastien Chevreux

Bastien Chevreux — Tue, 30 Apr 2013 14:23:13 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

Project Members:

Bastien Chevreux (admin)