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Related Concept Videos

Sanger Sequencing01:57

Sanger Sequencing

779.2K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Related Experiment Video

Updated: Apr 6, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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FermiKit: assembly-based variant calling for Illumina resequencing data.

Heng Li1

  • 1Genomics Platform, Broad Institute, Cambridge, MA 02142, USA.

Bioinformatics (Oxford, England)
|July 30, 2015
PubMed
Summary

FermiKit is a novel variant calling pipeline that de novo assembles whole-genome germline data. It accurately identifies genetic variations like SNPs and structural variations efficiently.

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Whole-genome sequencing generates vast amounts of data.
  • Accurate variant calling is crucial for genetic research.

Purpose of the Study:

  • To introduce FermiKit, a new variant calling pipeline.
  • To enable efficient and accurate variant detection from germline whole-genome data.

Main Methods:

  • De novo assembly of short reads from Illumina whole-genome germline data.
  • Mapping the assembly against a reference genome for variant identification.
  • Calling single nucleotide polymorphisms (SNPs), insertions/deletions, and structural variations.

Main Results:

  • FermiKit assembles 30-fold human whole-genome data in approximately one day on a 16-core server.

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Related Experiment Videos

Last Updated: Apr 6, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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  • Variant calling is completed in about 30 minutes.
  • Achieves accuracy comparable to current standard practices.

    • Conclusions:

    • FermiKit offers an efficient and accurate solution for germline variant calling.
    • The pipeline's assembly provides a concise data representation while preserving essential information.