I have an hybrid data of 454 + Illumina + SOLiD which i have assembled into 157439 contigs covering around 1.3 GB genome. Now I want to create scaffolds using 20kb (3 libraries) 454 paired end reads and BAC sequences.
Which tool can I use? I want to assemble genome of 850 MB.
As first selection, use MIRA3. But I will use combination of some tools because there is no perfect tool for any purposes.
The CLC Bio Genomics Workbench allows hybrid assemblies from these different sequencing technologies. I have personally done a hybrid assembly using Illumina and 454 sequence data....and I know they support SOLID data as well. I believe they have a 30 trial license that you can download.
I used the SSPACE software (http://www.baseclear.com/landingpages/sspacev12/) for the scaffolding. The contigs were obtained from illumina and 454 data and it worked well. If you want you could fill the gap with the Bowtie soft included in the archive available in the website.
The CLC software now allows the scaffolding but for project it didn't work well.
iAssembler package is also worth trying. This package combines MIRA, CAP3 and megablast in the pipeline. See more information from the link: http://www.biomedcentral.com/1471-2105/12/453/
To be able to assemble a complex genome it is critical to have an appropriate experimental design, particularly with genomes where there a large number of segmental duplications and/or high content of repetitive sequences. If you still have the opportunity to produce some more sequencing data it will be good to consider making sub-libraries from your target genome (e.g. isolate individual chromosomes) or ideally generate a BAC library and define a minimal tilling path to determine BAC pools that can be barcoded and sequenced in blocks of 1~10Mbp. This will reduce the complexity of a large 'complex' genome and the assembly process with the above mentioned tools should give you a better outcome.
Hi there,
can anyone that have used CLCbio genomics workbench, tell me the exact steps to perform an hybrid assembly using illumina and 454 data, please?
I am trying to find any kind of tutorial or set up protocol in oder t o do that.
Thanks
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