sinamajidian

phaseme

A tool set to assess the quality of the per read phasing and reduce the errors.

HapMC

NGS based haplotype assembly using matrix completion

MEC

Evaluating MEC

10xpipline

A pipline for haplotyping of 10x genomics

ads1-notebooks

Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing

ads1-slides

Slides for Algorithms for DNA Sequencing Coursera class

CreateFragmentMatrix

Convert input bam and vcf files to a fragment matrix

dendropy

graph-genomics-review

Precision pangenomics (review article on graph genomics)

GRFP

Here are a set of example Relevant Background and Future Goals and Graduate Research Plan Statement statements for the NSF GRFP in Ecology and Evolutionary Biology.

HapCUT2

software tools for haplotype assembly from sequence data

haplotyping_illumina

HapotypeAssembly

LRSIM

10x Genomics Reads Simulator

ml

phaseme_test

phaseme_test

polymc

ProbHap

Probabilistic single-individual haplotyping

Rcourse

An introduction to R programming

sdhapc

Improvement in SDhap code

WeightedMC