hapAssembly – Haplotype Assembly from Whole-Genome Sequence Data

hapAssembly

:: DESCRIPTION

hapAssembly  beats the previous best for the important Haplotype Assembly Problem. It is an approach to finding optimal solutions for the haplotype assembly problem under the minimum-error-correction (MEC) model.

::DEVELOPER

Chen Lab  & Lusheng Wang 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   hapAssembly

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 15;29(16):1938-45. doi: 10.1093/bioinformatics/btt349.
Exact algorithms for haplotype assembly from whole-genome sequence data.
Chen ZZ, Deng F, Wang L.

SEQERR – Estimates Genotype Error Rates for Whole-genome Sequence data

SEQERR

:: DESCRIPTION

The SEQERR program estimates the rate at which homozygous major allele genotypes are mis-called as heterozygote genotypes at low frequency markers. This error rate is estimated using observed allele and genotype frequencies at low frequency variants in identity by descent segments.

::DEVELOPER

Brian L. Browning 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

SEQERR

:: MORE INFORMATION

Citation:

Browning SR, Browning BL.
Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent.
Am J Hum Genet. 2015 Sep 3;97(3):404-18. doi: 10.1016/j.ajhg.2015.07.012. Epub 2015 Aug 20. PMID: 26299365; PMCID: PMC4564943.

MitoCounter 1.0.1 – Counting mitochondrial DNA Reads from Whole Genome Sequence

MitoCounter 1.0.1

:: DESCRIPTION

MitoCounter is a tool for counting mitochondrial DNA reads from Whole Genome Sequence

::DEVELOPER

Frank Hsueh-Ting Chu

:: SCREENSHOTS

MitoCounter

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MitoCounter

:: MORE INFORMATION

Citation

BMC Genomics. 2012;13 Suppl 7:S5. doi: 10.1186/1471-2164-13-S7-S5. Epub 2012 Dec 13.
Quantitative assessment of mitochondrial DNA copies from whole genome sequencing.
Chu HT, Hsiao WW, Tsao TT, Chang CM, Liu YW, Fan CC, Lin H, Chang HH, Yeh TJ, Chen JC, Huang DM, Chen CC, Kao CY.