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Related Concept Videos

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Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
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Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
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FastRemap: a tool for quickly remapping reads between genome assemblies.

Jeremie S Kim1, Can Firtina1, Meryem Banu Cavlak1

  • 1Department of Computer Engineering, ETH Zurich, D-ITET, Zurich 8006, Switzerland.

Bioinformatics (Oxford, England)
|August 17, 2022
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Summary
This summary is machine-generated.

FastRemap is a new tool that efficiently remaps genome reads between assemblies. It offers significant speedups and reduced memory usage compared to existing tools like CrossMap.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Genome remapping is crucial for analyzing large datasets.
  • Existing tools like CrossMap can be computationally demanding.

Purpose of the Study:

  • To develop a faster and more memory-efficient tool for remapping genome reads between assemblies.

Main Methods:

  • Developed FastRemap in C++.
  • Benchmarked FastRemap against CrossMap for speed and memory consumption.

Main Results:

  • FastRemap achieved up to 7.82x speedup (average 6.47x) compared to CrossMap.
  • FastRemap used as low as 61.7% (average 80.7%) of CrossMap's peak memory.
  • The tool is implemented in C++ for high performance.

Conclusions:

  • FastRemap offers a significant improvement in performance for genome read remapping.
  • The tool is freely available with source code, manual, and Docker image.