Applications

Applications/Tools the CCI is responsible for at MSKCC in CMO

Application	Location	Description
ACCESS-Pipeline	https://github.com/mskcc/ACCESS-Pipeline	This has workflows for BAM generation based on Marianas, Quality control generation, small variant calling, micro-satellite instabilty calling, copy number variant calling & structural variant calling for Version 1 of MSK-ACCESS assay
ACCESS_SV	https://github.com/mskcc/ACCESS_SV	This has the core workflow used for structural variant calling in MSK-ACCESS assay
ADMIE	https://github.com/mskcc/ADMIE	This is the algorithm used for calling MSI status for sample associated with MSK-ACCESS assay
Nucleo	https://github.com/msk-access/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)	https://github.com/msk-access/access_qc_generation	This is the version 2 of the ACCESS QC generation and you can read more about it hereMSK-ACCESS QC generation V2
ACCESS data analysis	https://github.com/msk-access/access_data_analysis	This repos helps with downstream data analysis of MSK-ACCESS data, you can read more about it here: space
Biometrics	https://github.com/msk-access/biometrics	Python package to calculate various sample contamination metrics. Biometrics
sequence_qc	https://github.com/msk-access/sequence_qc	Package for doing various ad-hoc quality control steps from MSK-ACCESS generated FASTQ or BAM files sequence_qc