Mira Assembler Manual

Sequence assembly with MIRA3 i Sequence assembly with MIRA3

The Definitive Guide

Sequence assembly with MIRA3 ii Copyright © 2010 Bastien Chevreux

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Sequence assembly with MIRA3 iii 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 iv 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? . . . . . . . . . . . . . . . . . .