# 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 %}