# 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

{% content-ref url="fundamentals/getting-set-up" %}
[getting-set-up](https://docs.cosap.bio/fundamentals/getting-set-up)
{% endcontent-ref %}

{% content-ref url="fundamentals/getting-set-up/cosap-via-docker" %}
[cosap-via-docker](https://docs.cosap.bio/fundamentals/getting-set-up/cosap-via-docker)
{% endcontent-ref %}

## Using COSAP Library

{% content-ref url="fundamentals/using-cosap" %}
[using-cosap](https://docs.cosap.bio/fundamentals/using-cosap)
{% endcontent-ref %}

## Using Web Application

{% content-ref url="fundamentals/using-the-web-app" %}
[using-the-web-app](https://docs.cosap.bio/fundamentals/using-the-web-app)
{% endcontent-ref %}

## Deploying COSAP Web Application and API

{% content-ref url="fundamentals/deploying-cosap" %}
[deploying-cosap](https://docs.cosap.bio/fundamentals/deploying-cosap)
{% endcontent-ref %}


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# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://docs.cosap.bio/cosap-comparative-sequencing-analysis-platform.md?ask=<question>
```

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The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.