> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/marianas/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/marianas/master.md).

# Introduction

Marianas is a java program used for generating accurate base calls from high-throughput sequencing data using Unique Molecular Identifier technology.

Since Marianas uses serial access over the entire bam file, it is highly efficient and processes all reads irrespective of target regions. Typically, Marianas collapsing for an MSK ACCESS sample would finish within 20 minutes, producing collapsed fastq files and QC metrics related to the collapsing process.

![Overview of the Marianas processing steps](/files/-M7JgMA5jxN84H420rxf)

This program was developed by [Juber Patel](https://github.com/juberpatel) in the [Center for Molecular Oncology](https://www.mskcc.org/research-programs/molecular-oncology) at [Memorial Sloan Kettering Cancer Center](https://cmo-ci.gitbook.io/marianas/www.mskcc.org). The source code for this tool can be found on the [Github page](https://github.com/mskcc/Marianas). Documentation has been compiled by [Juber Patel](https://github.com/juberpatel), [Ian Johnson](https://github.com/ionox0) with contributions from all members of [CMO Innovation lab](https://www.mskcc.org/research-programs/molecular-oncology/innovation-laboratory), [Berger Lab](https://www.mskcc.org/research-areas/labs/michael-berger), and [Clinical Bioinformatics groups](https://mskcc-clinbx.github.io/team/). 


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