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

# Applications



<table><thead><tr><th width="190.87900956668543">Application</th><th width="164.1821194828151">Location</th><th>Description</th></tr></thead><tbody><tr><td>ACCESS-Pipeline</td><td><a href="https://github.com/mskcc/ACCESS-Pipeline">https://github.com/mskcc/ACCESS-Pipeline</a></td><td>This has workflows for BAM generation based on <a href="https://app.gitbook.com/o/-LhMNgvjydB3TFWAUMVb/s/-M6GVE_FJ6Uok3BwY66L/">Marianas</a>, <a href="https://app.gitbook.com/o/-LhMNgvjydB3TFWAUMVb/s/-M52gq1rRSDQOKMQGEuR/">Quality control generation</a>, small variant calling, micro-satellite instabilty calling, copy number variant calling &#x26; structural variant calling for Version 1 of MSK-ACCESS assay</td></tr><tr><td>ACCESS_SV</td><td><a href="https://github.com/mskcc/ACCESS_SV">https://github.com/mskcc/ACCESS_SV</a></td><td>This has the core workflow used for structural variant calling in MSK-ACCESS assay</td></tr><tr><td>ADMIE</td><td><a href="https://github.com/mskcc/ADMIE">https://github.com/mskcc/ADMIE</a></td><td>This is the algorithm used for calling MSI status for sample associated with MSK-ACCESS assay</td></tr><tr><td>Nucleo</td><td><a href="https://github.com/msk-access/nucleo">https://github.com/msk-access/nucleo</a></td><td>This is the BAM generation workflow for any assay that deals with Unique Molecular Indexs (UMIs) based on <a href="http://fulcrumgenomics.github.io/fgbio/">Fgbio </a></td></tr><tr><td>ACCESS Quality Cotrol (For version 1 of the Assay)</td><td><a href="https://github.com/msk-access/access_qc_generation">https://github.com/msk-access/access_qc_generation</a></td><td>This is the version 2 of the ACCESS QC generation and you can read more about it here<a data-mention href="https://app.gitbook.com/o/-LhMNgvjydB3TFWAUMVb/s/-MbqIfOAQqfG2kMfi2uM-887967055/">MSK-ACCESS QC generation V2</a></td></tr><tr><td>ACCESS data analysis</td><td><a href="https://github.com/msk-access/access_data_analysis">https://github.com/msk-access/access_data_analysis</a></td><td>This repos helps with downstream data analysis of MSK-ACCESS data, you can read more about it here: <a data-mention href="broken-reference">Broken link</a></td></tr><tr><td>Biometrics</td><td><a href="https://github.com/msk-access/biometrics">https://github.com/msk-access/biometrics</a></td><td>Python package to calculate various sample contamination metrics. <a data-mention href="https://app.gitbook.com/o/-LhMNgvjydB3TFWAUMVb/s/-MOgRqoKNYiKeu3KYvC1-887967055/">Biometrics</a></td></tr><tr><td>sequence_qc</td><td><a href="https://github.com/msk-access/sequence_qc">https://github.com/msk-access/sequence_qc</a></td><td>Package for doing various ad-hoc quality control steps from MSK-ACCESS generated FASTQ or BAM files <a data-mention href="https://app.gitbook.com/o/-LhMNgvjydB3TFWAUMVb/s/-MBF_Q9ilpNTWJ9qRSgC/">sequence_qc</a></td></tr></tbody></table>

