1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
|
[](https://travis-ci.org/COMBINE-lab/salmon)
[](http://salmon.readthedocs.org/en/latest)
[](http://bioconda.github.io/recipes/salmon/README.html)
What is Salmon?
===============
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 *quasi-mapping* (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 *quasi-mapping* algorithm by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. an **unsorted** BAM file produced 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.
Give salmon a try! You can find the latest binary releases [here](https://github.com/COMBINE-lab/salmon/releases).
The current version number of the master branch of Salmon can be found [**here**](http://combine-lab.github.io/salmon/version_info/latest)
**NOTE**: Salmon works by (quasi)-mapping sequencing reads directly to the *transcriptome*. This means the Salmon index should be built on a set of target transcripts, **not** on the *genome* of the underlying organism. If indexing appears to be taking a very long time, or using a tremendous amount of memory (which it should not), please ensure that you are not attempting to build an index on the genome of your organism!
Documentation
==============
The documentation for Salmon is available on [ReadTheDocs](http://readthedocs.org), check it out [here](http://salmon.readthedocs.org).
Chat live about Salmon
======================
You can chat with the Salmon developers and other users via Gitter!
[](https://gitter.im/COMBINE-lab/salmon?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
|
