Tag: Salmon

Salmon v1.0.0 – Quantification of Transcript Abundance from RNA-seq reads

Salmon v1.0.0

:: DESCRIPTION

Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory. Salmon performs its inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

Salmon

:: MORE INFORMATION

Citation

Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford (2017).
Salmon provides fast and bias-aware quantification of transcript expression.
Nature Methods 14:417-419.

SAD – Salmon Anomaly Detection

SAD

:: DESCRIPTION

SAD detects the potential misquantifications for the RNA-seq transcript expression estimation made by Salmon. SAD detects large deviation of the observed coverage distribution from the expected coverage distribution for each transcript, and use the deviation as an indicator of misquantifications.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

SAD

:: MORE INFORMATION

Citation

Cong Ma, Carl Kingsford (2019).
Detecting, categorizing, and correcting coverage anomalies of RNA-seq quantification.
Cell Systems, in press..