Next-generation sequencing data analysis
This service has been terminated. We are not currently accepting applications.
The Human Genome Center (HGC) provides data analysis services for the Next Generation Sequencer (NGS) to support the establishment of a foundation for genome research in Japan. In particular, HGC will take full advantage of the HGC infrastructure to provide basic and advanced analysis services for ultra-fast NGS, based on the analysis pipelines in Nature, Science and other popular journals and optimized for supercomputers (for a fee). We also offer consulting services for medical and biological laboratories and companies that are considering acquiring data for next-generation sequencers on how to acquire the data necessary for their analysis.
Current services (including planned) are as follows For more complex analyses, please consult with us on a case-by-case basis. For more information, please contact the NGS analysis team at ngs_service@hgc.jp.
RNA-Seq
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Check sequencing results, such as adapter sequence removal, contaminant detection, and PCR duplicates.
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If a reference sequence is available, basic analysis of the read sequence against the reference genome is performed (e.g., mapping to the gene, analysis of the distribution of mapping positions on the gene, correlation analysis of coverage and GC content in the gene, detection of genes with different transcript lengths, etc.).
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In the absence of a reference sequence (in the case of de novo), the contig sequence is created by assembly of the read sequence, and the contig length is analyzed.
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It detects alternative splicing and compares transgenes between multiple samples.
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Perform more complex custom analysis.
De novo assembly
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Check sequencing results, such as adapter sequence removal, contaminant detection, and PCR duplicates.
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It takes advantage of the performance of the shared-memory supercomputer to perform the assembly and obtain the contig array.
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Basic analysis is performed (e.g. gene prediction, repeat region prediction, annotation of non-coding RNA prediction, etc.).
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Perform more complex custom analysis.
Exome-Seq
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Check sequencing results, such as adapter sequence removal, contaminant detection, and PCR duplicates.
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If a reference sequence is available, it is mapped to the reference genome.
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We perform basic analyses (e.g., quality control, histogramming of depth distribution in the target region, evaluation of uniformity and consensus, SNP/insertion/deletion analysis, analysis of sequencing depth and exon coverage, etc.).
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A more complex options analysis is performed.
DNA-Seq (Resequencing)
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Check sequencing results, such as adapter sequence removal, contaminant detection, and PCR duplicates.
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Mapping to the reference genome.
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Basic analysis is performed (e.g., SNP, insertion, deletion, structure variation, etc.)
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A more complex options analysis is performed.
miRNA-Seq
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Check sequencing results, such as adapter sequence removal, contaminant detection, and PCR duplicates.
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If a reference genome is available, the detected RNA sequence is mapped.
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We search for nearby complementary sequences on the mapped genome for potential duplexes.
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If mRNA information is available, the mRNA of the target is estimated.
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A more complex options analysis is performed.