Секвенирование следующего поколения (NGS)
Мы анализируем данные NGS, полученных с секвенаторов
— Illumina,
— Ion Torrent,
— 454,
— Solexa.

Принимаем данные в форматах FASTQ, FASTA или SFF.

Exome sequencing
Exome sequencing (also known as Whole Exome Sequencing, WES or WXS) is a technique for sequencing all the expressed genes in a genome. It consists of first selecting only the subset of DNA that encodes proteins (known as exons), and then sequencing that DNA using any high throughput DNA sequencing technology. There are 180,000 exons, which constitute about 1% of the human genome, or approximately 30 million base pairs.
Identify coding variants in population genetics, genetic disease, and cancer studies.

Trimmomatics, fastqc, bwa, bowtie, GATK, FREEC, samtools, bedtools etc.
Genome sequencing
Whole-genome sequencing is the most comprehensive method for analyzing the genome. Genomic information has been instrumental in identifying inherited disorders, characterizing the mutations that drive cancer progression, and tracking disease outbreaks. Rapidly dropping sequencing costs and the ability to produce large volumes of data with today's sequencers make whole-genome sequencing a powerful tool for genomics research
Identify inherited disorders, characterizing the mutations that drive cancer progression, tracking disease outbreaks, reveal methylation profile.

Trimmomatics, fastqc, bwa, bowtie, GATK, FREEC, samtools, bedtools etc
Transcriptome & microRNA
A transcriptome is the full range of messenger RNA, or mRNA, molecules expressed by an organism. In contrast with the genome, which is characterized by its stability, the transcriptome actively changes.
Provide gene expression profiles, which describe changes in the transcriptome in response to a particular condition or treatment.

Cufflinks, Bound, DESeq/edgR, Picard
Metagenomic data reveals the species composition of a microbial community and decoding its functional genes.
  1. For amplicon sequencing approach, the 16S rRNA gene has emerged as the most used marker. Further markers may be other rRNA genes, the ITS region, RuBisCo, mcrA or other functional genes.
  2. Metagenome sequencing (Shotgun Metagenomics for total DNA or Shotgun Metatranscriptomics for total RNA) offers a random representation of all extracted genomic sequences, giving insights into the metabolic profiles of these specific communities.
Diagnostic markers (gut metagenome, skin surface, stool, invaded tissues), environmental and bioremediations (soil, air, water samples), wastewater treatment, bioenergy (biogas consortia, anaerobic and aerobic degradation communities).

Trinity, Velvet, Blast, GeneMark, MEGAN, Qiime etc
Resistome and virulence factor
Resistome is a collection of all the antibiotic resistance genes in pathogenic and non-pathogenic bacteria. It includes resistance elements found in both pathogenic bacteria and antibiotic-producing bacteria, and cryptic resistance genes (which are not necessarily expressed) that are present in bacterial chromosomes.
Identification of genes resistant to antibiotics and level of resistance for specific organisms.

Fiona, Spades, quast, prokka, Mugsy, Prank, Mr. Bayes
Hi-C analysis
Hi-C is a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing.
Analyze genome-wide chromatin organization and reveal Topologically Associating Domains

Armatus, hiclib, Juicebox
Epigenetic modifications are reversible modifications on a cell's DNA or histones that affect gene expression without altering the DNA sequence. Two of the most characterized epigenetic modifications are DNA methylation and histone modification.
Regulation of gene expression, chromatine structure, splicing regulation

Bismark, BS-Seeker, histoneHMM, Genometricorr, StereoGene
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