Mira Assembler Manual

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  • Topic: DNA sequencing, Full genome sequencing, DNA
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Sequence assembly with MIRA3
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Sequence assembly with MIRA3

The Definitive Guide

Sequence assembly with MIRA3
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Copyright © 2010 Bastien Chevreux

This documentation is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.

Sequence assembly with MIRA3
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COLLABORATORS TITLE : Sequence assembly with MIRA3 ACTION NAME DATE SIGNATURE

WRITTEN BY

Bastien Chevreux

November 28, 2010

Extensive review of early reference manual

Jacqueline Weber

November 28, 2010

Extensive review of early reference manual

Andrea Hörster

November 28, 2010

Draft for section on preprocessing of ESTs in EST manual

Katrina Dlugosch

November 28, 2010

REVISION HISTORY NUMBER DATE DESCRIPTION NAME

Sequence assembly with MIRA3
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Contents

1 Introduction to MIRA3 1.1 1.2 1.3 1.4 What is MIRA? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

1 1 1 2 3 3 3 4 4 4 7

What to read in this manual and where to start reading?

The MIRA quick tour . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . For which data sets to use MIRA and for which not 1.4.1 1.4.2 1.4.3 Genome de-novo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Genome mapping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ESTs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

1.5

Any special features I might be interested in? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.5.1 1.5.2 1.5.3 1.5.4 1.5.5 1.5.6 1.5.7 MIRA learns to discern non-perfect repeats, leading to better assemblies . . . . . . . . . . . . . . . . . MIRA has integrated editors for Sanger, 454 and PacBio reads . . . . . . . . . . . . . . . . . . . . . .

MIRA lets you see why contigs end where they end . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 MIRA tags problematic decisions in hybrid assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . 15

MIRA allows older finshing programs to cope with amount of Solexa mapping data . . . . . . . . . . . 17 MIRA tags SNPs and other features, outputs result files for biologists . . . . . . . . . . . . . . . . . . . 19 MIRA has ... much more . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

1.6

Versions, Licenses, Disclaimer and Copyright 1.6.1 1.6.2

Versions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 License 1.6.2.1 1.6.2.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 MIRA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

1.6.3 1.6.4 1.7 1.8 1.9

Copyright . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 External libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Getting help / Mailing lists / Reporting bugs

Author . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Miscellaneous . . . . . . . . . . . . . . . . . . . . . . . . . . ....
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