salmon
wicked-fast transcript quantification from RNA-seq data
Install
- All systems
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curl cmd.cat/salmon.sh
- Debian
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apt-get install salmon - Ubuntu
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apt-get install salmon - Kali Linux
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apt-get install salmon - Windows (WSL2)
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sudo apt-get updatesudo apt-get install salmon - Dockerfile
- dockerfile.run/salmon
salmon
wicked-fast transcript quantification from RNA-seq data
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 different pipelines. For example, you can choose to make use of the 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.