Lancet is a somatic variant caller (SNVs and indels) for short read data. Lancet uses a localized micro-assembly strategy to detect somatic mutation with high sensitivity and accuracy on a tumor/normal pair. Lancet is based on the colored de Bruijn...

Contributors:  Michael Zody   Nicolas Robine   Giuseppe Narzisi   Andre Corvelo   Rajeeva Musunuri  


nygc-short-alignment-marking is a tool to mark short alignments in a bam file. It parses the bam and marks as unmapped a read with alignment length below a user-defined threshold. Reads are not filtered from the bam file but kept as...

Contributors:  Andre Corvelo  


Conpair is a fast and robust method dedicated for human tumor-normal studies to perform concordance verification (i.e. samples coming from the same individual), as well as cross-individual contamination level estimation in whole-genome and whole-exome sequencing experiments. Importantly, our method of...

Contributors:  Michael Zody  


taxMaps is an ultra-efficient, customizable and fully scalable taxonomic classification tool for short-read data designed to deal with large DNA/RNA metagenomics samples. Its performance and comprehensiveness makes it highly suitable for unbiased contamination detection in large-scale sequencing operations, microbiome studies...

Contributors:  Michael Zody   Nicolas Robine   Andre Corvelo   Wayne Clarke  


SCANVIS is a set of tools for SCoring, ANnotating and VISualizing splice junctions using gencode annotation. It scores splice junctions by using a Relative Read Support (RRS) measure that relates the reads supporting a query junction to reads supporting nearby annotated splice junctions....

SCANVIS visualization

Contributors:  Nicolas Robine   Heather Geiger  

NYGC Cancer Pipeline

NYGC's cancer pipeline identifies somatic and germline variants from whole genome sequencing (WGS), whole exome sequencing (WES) or targeted panel tumor and normal data. The pipeline can be run on sequencing data from human, mouse and patient-derived xenograft (PDX) models. Additionally,...

NYGC Somatic WGS v6 pipeline

Contributors:  Nicolas Robine   Tim Chu   Jennifer Shelton