Single-molecule Real-time DNA sequencing system PacBio RS II provides detecting complementary
DNA chain synthesis by a DNA-polymerase molecule at single-molecule level. This technology, based on
marked fluorescent nucleotides and high resolution confocal microscopy, allows real-time sequencing by
many polymerases simultaneously. The main advantage of the SMRT, or single molecule real time sequencing
technology is its huge read length: on average it comes to 4000 bp, although several reads can reach up
to 30 000 bp.
De novo genomes sequencing (including complex ones)
Hybrid sequencing of genomes (in cooperation with Illumina)
Sequencing quality and coverage uniformity analysis
Data filtering (adapters and low-quality reads removal)
De novo assembling
Reference reads mapping
Genomic data assays:
SNV search and annotation (single-nucleotide variations)
Somatic SNV search and annotation (single-nucleotide variations)
InDel (insertions and deletions) search and annotation
CNV search and annotation (copy number variations)
ncRNA search and annotation
Comparative genomic analysis
KEGG, Swissprot, GO, Nr and COG genes search and annotation
Gene families identification (for animals: TreeFam, for plants: OrthoMCL)
Association analysis: genotype-phonotype, haplotype-phenotype and genes interactions research
Species divergence time evaluation
Genetic maps constructing
LD (Linkage disequilibrium) analysis
Principal component analysis (PCA)
RNA data analysis:
Gene expression arrays (qualitative)
Gene expression arrays (quantitative)
New transcripts forecasting and annotation
miRNA, rRNA, tRNA, snRNA, etc. search by mapping in miRBase, Rfam и Genbank
New miRNAs and their secondary structures forecasting in Mireap
Search of transcripts, formed as a result of alternative splicing
Unigene GO classification
Metabolic pathways analysis
Differential expression analysis (for 2 and more samples)
General and specific transcripts search (for 2 and more samples)
Principal component analysis (PCA) (for 5 and more samples)
Methylation level calculation (individual sample)
Promoters and CpG-islands coverage analysis
Identification of deferentially methylated regions (for 2 and more samples)
Qualitative and quantitative analysis of species representation per sample
Reads mapping on bacterial, viral, fungal and archaeal genomes analysis
Chin, C. S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature methods. 2013. V. 10. P. 563-9.
2Koren, S., Schatz, M. C., Walenz, B. P., Martin, J., Howard, J. T., et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature biotechnology. 2012. V. 30. P. 693-700.
Huddleston, J., Ranade, S., Malig, M., Antonacci, F., Chaisson, M., et al. Reconstructing complex regions of genomes using long-read sequencing technology. Genome research. 2014. V. 24. P. 688-96.
Fang, G., Munera, D., Friedman, D. I., Mandlik, A., Chao, M. C., et al. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nature biotechnology. 2012. V. 30. P. 1232-9.
Zhang, W., Ciclitira, P. & Messing, J. PacBio sequencing of gene families - a case study with wheat gluten genes. Gene. 2014. V. 533. P. 541-6.