RVTESTS

Fast, handy association test software for family/unrelated studies and quantitative/binary trait. Single variant test (score test, Wald test), burden tests (CMC, SKAT, VT) are implemented. It also facilitate meta-analysis.

checkVCF

Validation software for VCF file (used in lipid consortium)

SEQMINER

Fast annotation software, and efficiently load and process VCF files.
This software is integrated into EPACTS

QPLOT

Quality check and visualize sequence alignment files

LASER

Ancestry inference using off-target reads (suitable for target/exome sequencing)

Polymutt

Family-based genotype caller

KARMA

Illumina and ABI SOLiD sequence reads aligner

ThunderVCF

Low-coverage genotype calling using Hidden Markov-chain Model (HMM)

VAMPr

To facilitate understanding of the connections between DNA variation and phenotypic AMR, we developed VAMPr (variant mapping and prediction of antibiotic resistance). It utilized 3,393 sequenced bacterial isolates from 9 species along with AMR phenotypes for 29 antibiotics following the Clinical & Laboratory Standards Institute (CLSI) guidelines. It also detected 14,615 variant genotypes and provided 93 association and prediction models.

Bayesian Integrative Model

A Bayesian model for the integrative analysis of microbiome data

FMAP

Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies