Alexis Dereeper, François Sabot

Analysis of NGS raw data with Galaxy

Cleaning, data control, alignment, polymorphism

Alexis Dereeper CIBA courses – Brasil 2011

Aim of the Tutorial classes:

1- Galaxy vs Command line

2- Understand FASTQ files

3- Cleaning of Illumina data (FASTQ)

4- Perform an assembly

5- Perform a mapping of Illumina reads on a reference sequence

6- Cleaning of a multiple SAM file

Alexis Dereeper, François SabotAlexis Dereeper CIBA courses – Brasil 2011

1- Galaxy

Serveur principal: http://main.g2.bx.psu.edu/

CIRAD Server : http://gohelle.cirad.fr/galaxy/

TOOLS DATA

WEB APPLICATION - “Click'n'Play” system- transparent for user

MODULAR- Numerous default bricks (already integrated)- Adding of customizable bricks

MULTIPLE- Based on a web server (Apache...)- On a single machine, or a cluster...

BUT- Simple support- Much less powerful than terminal- Only for routine analysis - Only for limited data

MULTIPLE- Based on a web server (Apache...)- On a single machine, or a cluster...

CONNECTION FOR THE TUTORIAL CLASSES:

http://gohelle.cirad.fr/galaxy/

Connecting...

Add data...

Import data from Galaxy libraries

FASTQ file → TEXT file

STRUCTURE:

@HWUSI-EAS454_0006:1:112:14105:5498#CTTGTACGCCAAGAAGTGTAGCAAAACGGCAGAGCTCGTGGATTAAACAAACAGAGGATTTCGGTGAGGATTGAGGGGGAGT

+cfffcfeffdeefefffcffffffffcffeffffdffffafcfffffdffffdfefeddf^eececfffdfcbffb

@HWUSI-EAS454_0006:1:37:16314:3410#CTTGTAAGTGTAGCAAAACGGCAGAGCTCGTGGATTAAACAAACAGAGGATTTCGGTGAGGATTGAGGGGGAGTGGTGGCCG

+`bTbbccccceeeeeceeeecccYeedded`ceec]dddde^a`deeeec\`dddcbaadadYd`]]Jc_^bc^^\