2127 days ago
Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly...2013 days ago
HipSTR: Haplotype inference and phasing for Short Tandem Repeats
...g data Employing a specialized hidden Markov model to align reads to candidate alleles while accounting for STR artifacts Utilizing phased SNP haplotypes to genotype and phase STRs...1880 days ago
geck: trio-based comparative benchmarking of variant calls
Determine the accuracy of our model by comparing the precision and recall of GATK Unified Genotyper and Haplotype Caller on the high-confidence SNPs of the NIST Ashkenazim trio and the...1807 days ago
HaploTypo: a variant-calling pipeline for phased genomes
...reasing number of phased (i.e. with resolved haplotypes) reference genomes are avail...calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyse...1593 days ago
SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
SVEngine (Structural Variants Engine) SVEngine is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various ty...1395 days ago
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a huma.... It also introduces a new graph binning algorithm and achieves the best haplotype-resolved assembly given trio...1222 days ago
Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
...obscure genomes with duplications, various ploidy levels, etc. Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous...794 days ago