De-Novo Genome Sequencing
NGB diagnostics offers multiple tiers of de-novo genome sequencing and assembly portfolio to help you achieve your de-novo genome sequencing project goals for a reasonable price. Whether you are starting with raw material or need help analyzing data produced elsewhere, let our team of experienced scientists help.
We currently offer multiple sequencing platforms including Pacific Biosciences (PacBio) Sequel, Illumina HiSEQ4000 & X10, BioNano IRYS Mapping, and Ion Torrent. We have following options for various levels of services near complete draft genomes to chromosome level genome services.
Platinum Genome
- Genome backbone: 30x Pacbio Sequel or nanopore ultra long read data.
- Genome error correction: 80-100x Illumina short read data (150x2bp reads).
- Scaffolding: 100x data Bionano IRYS mapping or Hi-C data.
- Pseudomolecules: GBS/ddRAD based biparental Linkage Mapping on 96 samples and further scaffolding of scaffolds into pseudomolecules.
Standard Bioinformatics includes:
- Hybrid assembly
- Scaffolding
- Pseudomolecule generation.
- Genome Annotation & Comparative Genomics
- Gene prediction & annotation using: Ab-initio, homology based, cDNA based.
- BLASTP alignment to KEGG, SwissProt, and TrEMBL databases.
- Motifs and domains using InterProScan against protein databases, including ProDom, PRINTS, Pfam, SMART, PANTHER, and PROSITE.
- non-coding RNA (ncRNA) prediction, rRNA, transfer RNAs (tRNAs), snRNA and microRNAs annotations.
- Syntenic blocks and gene collinearity analysis with 6 major plant species. Synonymous (Ks) and non-synonymous (Ka) substitution rates for orthologous gene pairs.
- Phylogenomics analysis for sequenced land races/ wild populations to identify selective sweeps. IBD analysis. LD analysis. Population structure analysis.
