> For the complete documentation index, see [llms.txt](https://docs.cosap.bio/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.cosap.bio/cosap-comparative-sequencing-analysis-platform.md).

# COSAP - Comparative Sequencing Analysis Platform

## Overview

COSAP is a sequencing analysis platform that encapsulates a python library, a web application and API to provide users a hassle next generation sequencing data analysis.

A typical variant calling pipeline consists of Read Trimming, Read Mapping, Duplicate Removal\&Base Calibration, Variant Calling and Variant Annotation steps. COSAP provides several tool options for each of these steps.

## Get Started

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[Getting Set Up](/fundamentals/getting-set-up.md)
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[COSAP via Docker](/fundamentals/getting-set-up/cosap-via-docker.md)
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## Using COSAP Library

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[Using COSAP](/fundamentals/using-cosap.md)
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## Using Web Application

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[Using the Web App](/fundamentals/using-the-web-app.md)
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## Deploying COSAP Web Application and API

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[Deploying COSAP](/fundamentals/deploying-cosap.md)
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