fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Whole Genome Sequencing analysis, WGS analysis

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Call and score variants from WGS/WES of rare disease patients.

Rapid determination of appropriate reference genomes.

Snakemake-based workflow for detecting structural variants in genomic data

A comprehensive cancer DNA/RNA analysis and reporting pipeline

Analysis pipelines for genomic sequencing data

A tool to genotype CYP2D6 with WGS data

Data management of large-scale whole-genome sequence variant calls using GDS files (Development version only)

Kourami: Graph-guided assembly for HLA alleles

Workflow to construct linear representation of pan genome from deep WGS data and public assemblies

Integrated copy number variation detection toolset

Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS

A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.

vSNP -- validate SNPs

Targeted Detection and Reconstruction of Plasmids

Exome/Capture/RNASeq Pipeline Implementation using snakemake

A snakemake workflow for WGS-based tuberculosis transmission analysis

Trim, Align to genome, Deduplicate, Realign WGS sequencing samples