Next Generation Sequencing (NGS) is a frequently applied approach to detect sequence variationsbetween highly related genomes. Recent large-scale re-sequencing studies as the Human 1000 GenomesProject utilize NGS data of low coverage to afford sequencing of hundreds of individuals. Here, SNPsand micro-indels can be detected by applying an alignment-consensus approach. However,computational methods capable of discovering other variations such as novel insertions or highlydiverged sequence from low coverage NGS data are still lacking.
Results
We present LOCAS, a new NGS assembler particularly designed for low coverage assembly of eukaryotic genomes using a mismatch sensitive overlap-layout-consensus approach. LOCAS assembles homologous regions in a homology-guided manner while it performs de novo assemblies of insertions and highly polymorphic target regions subsequently to an alignment-consensus approach. LOCAS has been evaluated in homology-guided assembly scenarios with low sequence coverage of Arabidopsis thalianastrains sequenced as part of the Arabidopsis 1001 Genomes Project. While assembling the same amount of long insertions as state-of-the-art NGS assemblers, LOCAS showed best results regarding contig size, error rate and runtime.
Conclusion
LOCAS produces excellent results for homology-guided assembly of eukaryotic genomes with short readsand low sequencing depth, and therefore appears to be the assembly tool of choice for the detection ofnovel sequence variations in this scenario.
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This is a great and nice answer! Thanks Michael! But, top banrds are underrepresented in Brazil. Most solution specialists are friends of mine from grad/undergrad times. For instance, IBM regularly hires people like myself for solution deployment, validation and maintenance. There are very few HPC (official) vendors, too. Our connection is already fibre (nice!!!). It’s good to hear that in the end bioinformatics data are not so different. I’ll talk with other sysadmins right now. The system accepts hotswap already. Using ext4. I’m not very comfortable with cryptography. Any recomendation? Mar 25 2010 at 11:59
Hmm, maybe not the worst idea to buy a ready-made rack from e.g. HAL, Sun/Oracle, but of course, it’s maybe hard to find the reietlar of your trust. Reg. bioinformatics data, maybe the main difference in the future (high-th. seq, -omics) is that one has to make the decision, which data you can afford to store and which you can afford to throw away. That’s the bioinformatics decision. Also transfer of a TB data from sequencer to storage is a problem. Some sequencers (eg 454 titanium) have compute clusters attached that due the processing and (temp.) storage. Mar 25 2010 at 21:23
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