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TakeABreak (version 1.1.0)

Select your usage:

Read file:

Raw reads as input

length of the k-mers:

Set the length of used kmers

solidity threshold:

abundance threshold for solid kmers

local complexity threshold:

the local complexity threshold

max similarity percentage:

Inversions with a and b' (or u and v') whose longest common subsequence size is bigger than k*(this value)/100 are discarded

maximal repeat size:

maximal repeat size at the breakpoint. Longest common suffix between a and b

Description

TakeABreak is a tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes. Its implementation has a very limited memory impact allowing its usage on common desktop computers and acceptable runtime (Illumina reads simulated at 2x40x coverage from human chromosome 22 can be treated in less than two hours, with less than 1GB of memory).

Web site

http://colibread.inria.fr/takeabreak/

Integrated by

Yvan Le Bras and Cyril Monjeaud

GenOuest Bio-informatics Core Facility

UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)

support@genouest.org

If you use this tool in Galaxy, please cite :

Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013.