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Fungal Whole Genome Resequencing


Fungal whole genome resequencing refers to the high-throughput sequencing of fungal individuals or populations with the availability of a reference genome. We provide the fungal whole genome resequencing platform to help you mine a large number of single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), structural variations (SVs), and copy number variations (CNVs) in the fungal genomes.

Our Advantages:
  • Advanced sequencing platforms: Illumina HiSeq, Nanopore MinION, and PacBio SMRT platforms.
  • Cloud-based platform for bioinformatics analysis.
  • Rapid, efficient, flexible workflow for sequencing and data analysis.
  • Extensive experience in the industry of genomic service.
  • Keep up with the frontiers of microbial genomics and bioinformatics analysis.
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Introduction to our fungal whole genome resequencing platform

We provide fungal whole genome resequencing using a whole-genome shotgun strategy by next generation sequencing (Illumina HiSeq PE150/251, 100X) or long-read sequencing platforms (PacBio RSII or Nanopore MinION instrument). A large amount of reads generated from sequencers are subjected to quality control, and the clean data are subsequently aligned to reference genome sequences. With powerful bioinformatics analysis, we can detect a large number of variations including SNPs, InDels, SVs, CNVs, etc. Fungal whole genome resequencing is an effective, accurate, and rapid method for sequencing and analyzing fungal genomes.

With the increasing of high-quality reference genome sequences that are available for different species, the application of fungal genome resequencing become more widespread. Fungal whole genome resequencing can quickly and efficiently detect both mutations and structural variations on a global genome. Comparative genomic analysis is provided to identify differentially expressed genes through gene ontology analysis and explore the evolutionary relationships and biological traits, including pathogenic mechanism and resistant mechanism. Moreover, our platform supports multiple fields, including pharmaceutical and biotechnology industries, scientific research, clinical applications, agriculture, etc.

Microbial diversity analysis workflow

Bioinformatics Analysis

Our bioinformatics analysis includes: genomic assembly, genomic structure studies, functional annotation and comparative genomic analysis. For advanced bioinformatics analysis in detail, please refer to the following table.

Genomic Assembly Data quality control
Raw data filtering
Sequence alignment
Genomic Structure Analysis Detection of SNPs, InDels, SVs, CNVs
Detection of CRISPRs
LncRNA prediction
Functional Annotation NR, GO, COG, KEGG, SwissProt, Pfam, TCDB, SignalP, CAZy
Comparative Genomic Analysis Synteny analysis
Analysis of gene family evolution
Phylogenetic analysis
ANI analysis

Sample Requirement

Sampling kits: We provide a complete range of microbial sampling kits for clients, including microbial collection products, DNA/RNA isolation kits, and accessories for storage and mailing.

Deliverables: Raw sequencing data (FASTQ), annotated sequences (FASTA), quality-control dashboard, statistic data, and the bioinformatics report.

References

  1. Bentley D R. Whole-genome re-sequencing. Current opinion in genetics & development, 2006, 16(6): 545-552.
  2. Li R, Li Y, Fang X, et al. SNP detection for massively parallel whole-genome resequencing. Genome research, 2009, 19(6): 1124-1132.

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