Most of my software as well as vignettes and scripts for the analyses connnected to my research can be found on my GitHub page. I maintain the following software packages:

• Monopogen (Single nucleotide variant calling from single cell sequencing)

Monopogen is developed to achieve SNV calling from single cell RNA sequencing, single cell ATAC sequencing.

• BindSC (Bi-order integration of single cell multi-omics data)

This tool is developed to achive bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data.

• WEScall (A genotype calling pipeline for whole exome sequencing (WES) data)

WESCall can analyze both target and off-target data, and is a useful tool to facilitate WES sutides with decent amount of off-target data.

• SEEKIN(Sequencing-based estimation of kniship and inbreeding coefficients)

This program estimates the kinship and inbreeding coefficients based on extremely low-sequencing coverage datasets (typically lower than 0.5X).

• AMMO(An integrated package for whole-genome restriction mapping and genome scaffolding)

This is an integrated program that generates 2b-RAD-based restriction maps for scaffolding draft genome assemblies produced by using short Illumina reads or long PacBio reads.

• RADTyping(De novo RAD Genotyping in Mapping Populations)

This is an integrated package for accurate De Novo codominant and dominant RAD genotyping in mapping populations.