Applications/Tools the CCI is responsible for at MSKCC in CMO
Application | Location | Description |
---|---|---|
ACCESS-Pipeline
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 Fgbio
ACCESS Quality Cotrol (For version 1 of the Assay)
ACCESS data analysis
Biometrics
sequence_qc
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
This is the version 2 of the ACCESS QC generation and you can read more about it here
This repos helps with downstream data analysis of MSK-ACCESS data, you can read more about it here:
Python package to calculate various sample contamination metrics.
Package for doing various ad-hoc quality control steps from MSK-ACCESS generated FASTQ or BAM files