https://github.com/msk-access/access_data_analysis

Scripts for downstream analysis plotting of pipeline output

analysis data-analysis msk-access python r

Last synced: 10 Feb 2026

https://github.com/msk-access/merge_fastq

Package to merge multiple pair of pair-end fastq data

fastq-files

Last synced: 10 Feb 2026

https://github.com/msk-access/nucleo

Workflow that creates all the BAM files for the cfDNA assay based FASTQ file at MSK

bam msk-access umi

Last synced: 10 Feb 2026

https://github.com/msk-access/cwl_subworkflows

A list of subworkflows used for MSK-ACCESS data processing.

common-workflow-language cwl-workflow workflow

Last synced: 10 Feb 2026

https://github.com/msk-access/genotype_variants

Project to genotype SNV, INDEL and SV.

genotyping msk-access

Last synced: 10 Feb 2026

https://github.com/msk-access/gbcms

A high-performance orientation-aware genotype counting system for genomic variants

Last synced: 15 May 2026

https://github.com/msk-access/nucleo_qc

Quality Control Workflow for UMI based BAMs

cfdna chip

Last synced: 10 Feb 2026

https://github.com/msk-access/kreview

Advanced cfDNA Fragmentomics Core Evaluation Engine

Last synced: 05 Jun 2026

https://github.com/msk-access/chip-var

Workflow for calling and annotating CHIP variants

Last synced: 10 Feb 2026

https://github.com/msk-access/py-gbcms

high-performance tool for extracting base counts and variant metrics from BAM files.

Last synced: 24 Feb 2026

https://github.com/msk-access/uncollapsed_bam_generation

Workflow for making MSK-ACCESS standard binary alignment mapping file.

cfdna ctdna cwl cwl-workflow umi workflow

Last synced: 10 Feb 2026

https://github.com/msk-access/bam_collapsing

Workflow for collapsing of standard binary alignment mapping file generated by MSK-ACCESS

bam-collapsing ctdna cwl-workflow duplex fgbio msk-access workflow

Last synced: 10 Feb 2026