Question: Genome Rearrangement Detection (From Short Reads Alignment Or Genome Alignment)
3
gravatar for Leszek
8.8 years ago by
Leszek4.0k
IIMCB, Poland
Leszek4.0k wrote:

I'm looking for a tools that detect structural variations (SVs, genome rearrangement) between sequenced genome and its reference.

I have got 45 bp paired-ends reads (Illumina HiSeq), ~40x coverage from 13Mb haploid yeast strain.

I know that there are some tools that can estimate SVs from reads alignments (eg SVDetect, BreakDancer). Another approach is to align de novo assembly onto reference genome and get SVs from there (eg Mummer). I would like you know, which is better approach, and how would you do it ideally? Maybe someone has got ready pipeline for that?

ADD COMMENTlink modified 5.5 years ago by mesabioinformatics30 • written 8.8 years ago by Leszek4.0k
1
gravatar for Casey Bergman
8.8 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

Here are a couple of tools for SV detection you may want to look into that I've been reading about lately (just today!), but haven't tried:

Any feedback on how these systems perform would be helpful for the community.

ADD COMMENTlink written 8.8 years ago by Casey Bergman18k
1
gravatar for Adrian Pelin
5.8 years ago by
Adrian Pelin2.4k
Canada
Adrian Pelin2.4k wrote:

I myself have not tried using any of these tools, but this type of analysis is in my TODO list. I found this a couple of days ago and it looks very promising:

http://bioinf.spbau.ru/en/sibelia

From their website:

Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.

Sibelia is useful in finding: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to other genomes.

In version 2, Sibelia works with multiple strains of bacteria and partitions their genomes into synteny blocks — blocks of highly conserved regions among all compared genomes. It represents genomes in circos pictures [for publication] or interactive forms [for experts’ analysis].

Sibelia is under active development. If you see that Sibelia has a potential to support your research, please do not hesitate to contact us at vyahhi@bioinf.spbau.ru with a list of features you would like Sibelia to have.

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Adrian Pelin2.4k
1

Thanks! (+1). Will Sibelia work for larger organisms like plants? I also asked a similar question here.

ADD REPLYlink written 4.4 years ago by hbw70
0
gravatar for brentp
8.8 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

You might have a look at breakway ("Identify Structural Variations in Genomic Data").

ADD COMMENTlink written 8.8 years ago by brentp23k
2

I've tried breakway and breakdancer as well. I was really surprised, that these programmes give completely inconsistent results! Could anyone comment on that?

ADD REPLYlink written 8.8 years ago by Leszek4.0k
0
gravatar for mesabioinformatics
5.5 years ago by
United States
mesabioinformatics30 wrote:

Even Sibelia has a web interface:

https://etool.me/software/sibelia

https://etool.me/software/csibelia

ADD COMMENTlink written 5.5 years ago by mesabioinformatics30
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