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Statistics & machine learning
We analyze NGS that performed by common sequencing machines:
— Illumina,
— Ion Torrent,
— 454,
— Solexa.

Data is provided in FASTQ, FASTA or SFF format.

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.
Application
Identify coding variants in population genetics, genetic disease, and cancer studies.

Tools
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
Application
Identify inherited disorders, characterizing the mutations that drive cancer progression, tracking disease outbreaks, reveal methylation profile.

Tools
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. The term "transcriptome" can also be used to describe the array of mRNA transcripts produced in a particular cell or tissue type. In contrast with the genome, which is characterized by its stability, the transcriptome actively changes. In fact, an organism's transcriptome varies depending on many factors, including stage of development and environmental conditions.
Microarrays!!!
Application
Provide gene expression profiles, which describe changes in the transcriptome in response to a particular condition or treatment.

Tools
Cufflinks, Bound, DESeq/edgR, Picard
Metagenomics
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.
Application
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).

Tools
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.
Application
Identification of genes resistant to antibiotics and level of resistance for specific organisms.

Tools
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.
Application


Tools

Methylation
Hi-C is a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing.
Application


Tools

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