HapCHAT

HapCHAT is a haplotype assembly method that improves existing techniques for handling long reads and higher coverages. It is equipped with a unique algorithm that adjusts the estimated number of errors at each variant site to minimize the number of error corrections needed to find a feasible solution.

Topic

Sequencing

Detail

  • Operation: Haplotype mapping

  • Software interface: Graphical user interface

  • Language: C++;Python

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: -

  • Credit: -

  • Input: genome.fasta, file.bam,file.vcf

  • Output: out.realigned.phased.vcf, out.phased.vcf

  • Contact: murray.patterson@unimib.it

  • Collection: -

  • Maturity: -

Publications

  • HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads.
  • Beretta S, et al. HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads. HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads. 2018; 19:252. doi: 10.1186/s12859-018-2253-8
  • https://doi.org/10.1186/s12859-018-2253-8
  • PMID: 29970002
  • PMC: PMC6029272

Download and documentation

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