Applications

ACCESS-Pipeline

This has workflows for BAM generation based on , , small variant calling, micro-satellite instabilty calling, copy number variant calling & structural variant calling for Version 1 of MSK-ACCESS assay

ACCESS_SV

This has the core workflow used for structural variant calling in MSK-ACCESS assay

ADMIE

This is the algorithm used for calling MSI status for sample associated with MSK-ACCESS assay

Nucleo

This is the BAM generation workflow for any assay that deals with Unique Molecular Indexs (UMIs) based on

ACCESS Quality Cotrol (For version 1 of the Assay)

This is the version 2 of the ACCESS QC generation and you can read more about it here

ACCESS data analysis

This repos helps with downstream data analysis of MSK-ACCESS data, you can read more about it here:

Biometrics

Python package to calculate various sample contamination metrics.

sequence_qc

Package for doing various ad-hoc quality control steps from MSK-ACCESS generated FASTQ or BAM files