Microindel detection in short-read sequence data

No abstract is available for this paper.

• Publication year

  2010

• Venue

  Bioinform.

• Publication date

  2010-03-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btq027PMID 20144947
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2010influential reference
• The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group.

  2009cited by this paper
• knowledge-based potentials and structural filters Coarse-grained modeling of large RNA molecules with Material Supplemental

  2009cited by this paper
• Evaluation of next generation sequencing platforms for population targeted sequencing studies

  2009cited by this paper
• Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

  2009cited by this paper
• RazerS--fast read mapping with sensitivity control.

  2009cited by this paper
• Mapping short DNA sequencing reads and calling variants using mapping quality scores.

  2008cited by this paper
• Next-generation DNA sequencing methods.

  2008cited by this paper
• Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry

  2008cited by this paper
• The complete genome of an individual by massively parallel DNA sequencing

  2008cited by this paper
• Sequencing of natural strains of Arabidopsis thaliana with short reads.

  2008cited by this paper
• The Diploid Genome Sequence of an Individual Human

  2007influential reference
• Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome

  2007cited by this paper
• Global variation in copy number in the human genome

  2006cited by this paper
• Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes.

  2005cited by this paper
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  2005cited by this paper
• Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity

  2005cited by this paper
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  2004cited by this paper
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  2003cited by this paper
• Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites.

  2003cited by this paper
• mreps: efficient and flexible detection of tandem repeats in DNA

  2003cited by this paper
• Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids

  1998cited by this paper

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• VarSCAT: A computational tool for sequence context annotations of genomic variants

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  2020cites this paper
• Rare and de novo coding variants in chromodomain genes in Chiari I malformation.

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