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Repository salmon
Name: salmon
Owner: bgruening
Synopsis: Salmon quant function from the 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. Alevin adds to this functionality with a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing
 data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell
 barcode whitelisting.
Type: unrestricted
Revision: 5:53e9709776a0
This revision can be installed: True
Times cloned / installed: 3159

Contents of this repository

Name Description Version Minimum Galaxy Version
Transcript Quantification from RNA-seq data 0.8.2 any

Categories
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
RNA - Utilities for RNA