Software

Software

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RVTESTS

Description

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.

Software Package rvtests
 

 

checkVCF

Description

Validation software for VCF file (used in lipid consortium)

Software Package  checkVCF

 

SEQMINER

Description

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

Software Package seqMiner

 

QPLOT

Description

Quality check and visualize sequence alignment files

Software Package QPLOT

 

LASER

Description

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

Software Package LASER

 

Polymutt

Description

Family-based genotype caller

Software Package Polymutt

 

KARMA

Description

Illumina and ABI SOLiD sequence reads aligner

Software Package karma

 

ThunderVCF

Description

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

Software Package Developing

 

VAMPr

Description

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.

Website https://cdc.biohpc.swmed.edu/VAMPr/VAMPr.cgi

 

Bayesian Integrative Model

Description

A Bayesian model for the integrative analysis of microbiome data

Website
https://shuangj00.github.io/IntegrativeBayes/articles/Tutorial.html

 

FMAP

Description

Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies

Website https://qbrc.swmed.edu/FMAP/