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[![Build Status](https://travis-ci.org/COMBINE-lab/salmon.svg?branch=master)](https://travis-ci.org/COMBINE-lab/salmon) | ||
[![Documentation Status](https://readthedocs.org/projects/sailfish/badge/?version=develop)](https://readthedocs.org/projects/sailfish/?badge=develop) | ||
[![Documentation Status](https://readthedocs.org/projects/salmon/badge/?version=latest)](https://readthedocs.org/projects/salmon/?badge=latest) | ||
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What is Salmon? | ||
=============== | ||
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Salmon is a **wicked**-fast program to produce a highly-accurate, transcript-level quantification estimates from | ||
RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the | ||
use of *lightweight* alignments (accurate but fast-to-compute proxies for traditional read alignments) and | ||
massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely | ||
into many differnt pipelines. For example, you can choose to make use of our *lightweight* alignments by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. | ||
computed with your favorite aligner), and it will use the same **wicked**-fast, state-of-the-art inference algorithm | ||
to estimate transcript-level abundances for your experiment. | ||
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Documentation | ||
============== | ||
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The documentation for Salmon is available on [ReadTheDocs](http://readthedocs.org), check it out [here](http://salmon.readthedocs.org). | ||
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Chat live about Salmon | ||
====================== | ||
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You can chat with the Salmon developers and other users via Gitter! | ||
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[![Join the chat at https://gitter.im/COMBINE-lab/salmon](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/COMBINE-lab/salmon?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) | ||
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Documentation | ||
============== | ||
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The documentation for Salmon is available on [ReadTheDocs](http://readthedocs.org), check it out [here](http://sailfish.readthedocs.org). |