Illumina mate-pair reads with TakeABreak

Question

[vincenzo.bonnici]

Hi, is there any way to let TakeABreak working on Illumina mate pair reads? If not, is there a consolidated pipeline that I can use to preprocess my reads for using them in TakeABreak?

Thank you.

[Brian Bushnell]

Perhaps you could provide a link to TakeABreak, or explain what it is you are trying to do?

[vincenzo.bonnici]

TakeABreak is a tool developed on top of GATB https://gatb.inria.fr/software/takeabreak/

It takes the advantages of the succinct representation of De Bruijn graph provided by GTAB in order to find breakpoints of genomic structural variants, in particular inversions.

It think the missing feature also affect the GATB core library that is able to build the graph only from single reads.

I just would like to understand if there is some common approach,

Thank you.

Answer 1

[claire.lemaitre]

Hi,

TakeABreak can use paired-end and mate pair reads as well as single-end ones, it just does not use the pairing or mating information. You can indicate in the input that some fastq files come from the same sample, using files of files (fof). For instance, if you have three samples, each represented by two files (one for each mate), you can run TakeABreak as follows:

./TakeABreak -in path/DATA/data_3indiv.fof

The file data_3indiv.fof contains 3 lines such as :

indivA.fof
indivB.fof
indivC.fof

With indivA.fof file, being located in the path/DATA directory and containing the following two lines :

indivA_readR1.fastq
indivA_readR2.fastq

This is documented in TakeABreak Readme : https://github.com/GATB/TakeABreak and this is a feature of the GATB-core library, so you can do this for a majority of tools developped on top of GATB.

I hope this answers your question.