Longshot v0.43 – Diploid SNV Caller for Error-prone Reads

Longshot v0.43

:: DESCRIPTION

Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also genotype and phase input VCF files. It can output haplotype-separated BAM files that can be used for downstream analysis.

::DEVELOPER

Bansal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Longshot

:: MORE INFORMATION

Citation

Edge P, Bansal V.
Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing.
Nat Commun. 2019 Oct 11;10(1):4660. doi: 10.1038/s41467-019-12493-y. PMID: 31604920; PMCID: PMC6788989.

maxdip – Estimating Cross-over and Gene Conversion Rates from Diploid unphased Polymorphism data

maxdip

:: DESCRIPTION

maxdip is a software to estimate rho (4Nr) and gene conversion rates  using random samples with two-site  unphased diploid information. The estimate is obtained by a maximum composite likelihood method based on pairs of sites,

::DEVELOPER

Richard R. Hudson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 maxdip

:: MORE INFORMATION

Citation:

Hudson, R. R. (2001)
Two-locus sampling distributions and their application.
Genetics 159: 1805-1817

PedigreeSim – Simulation of Genotypes in Pedigrees of Diploid and Tetraploid Species

PedigreeSim

:: DESCRIPTION

PedigreeSim is software that generates simulated genetic marker data of individuals in pedigreed populations. A population can consist of either diploid or tetraploid individuals. PedigreeSim can simulate meioses with or without chiasma interference, and in tetraploids it can simulate meioses with two bivalents or one quadrivalent per set of hom(oe)ologous chromosomes. Also varying probabilities of preferential versus random pairing of chromosomes can be simulated, allowing to simulate amphidiploids as well as autotetraploids and intermediate forms.

::DEVELOPER

Wageningen UR Plant Breeding

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ MacOsX / Linux
  • Java

:: DOWNLOAD

 PedigreeSim

:: MORE INFORMATION

Citation

Voorrips RE, Maliepaard CA (2012)
The simulation of meiosis in diploid and tetraploid organisms using various genetic models.
BMC Bioinformatics. 2012 Sep 26;13:248.