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Alignment-free isoform quantification software tools | RNA-seq analysis

Traditional quantification algorithms that use alignments of sequencing reads to the genome or transcriptome require substantial computational resources (Teng et al., 2016) and do not scale well with the rate at which data are produced (Kodama et…
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Sailfish
Desktop

Sailfish

Performs isoform quantification from RNA-seq data. Sailfish is an open source…

Performs isoform quantification from RNA-seq data. Sailfish is an open source software developed for reducing parametric complexity, by avoiding mapping reads. The application first constructs an…

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Sailfish-cir
Desktop

Sailfish-cir

Estimates the relative abundance of circular RNA transcripts from…

Estimates the relative abundance of circular RNA transcripts from high-throughput RNA-seq data. Sailfish-cir transforms circular transcripts to pseudo-linear transcripts. Comparing to count-based…

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Arkas
Server

Arkas

Allows reproducible RNAseq analysis. Arkas is a cloud computational pipeline…

Allows reproducible RNAseq analysis. Arkas is a cloud computational pipeline that encapsulates Kallisto, automates the construction of composite transcriptomes from multiple sources, quantifies…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

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TCW
Desktop

TCW Transcriptome Computational Workbench

A software package for assembling, annotating, querying, and comparing…

A software package for assembling, annotating, querying, and comparing transcript and expression level data.

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RNA-Skim
Desktop

RNA-Skim

A RNA-Seq quantification method which partitions the transcriptome into…

A RNA-Seq quantification method which partitions the transcriptome into disjoint transcript clusters based on sequence similarity, and introduces the notion of sig-mers, which are a special type of…

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Salmon
Desktop

Salmon

A tool for quantifying the expression of transcripts using RNA-seq data. Salmon…

A tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the novel concept of lightweight alignment with a streaming inference…

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kallisto
Desktop

kallisto

Allows users to quantify abundances of transcripts from RNA-Seq data and target…

Allows users to quantify abundances of transcripts from RNA-Seq data and target sequences using high-throughput sequencing (HTS) reads. kallisto is based on pseudo-alignment concept to determine the…

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bcbio-nextgen
Desktop

bcbio-nextgen

A python toolkit providing best-practice pipelines for fully automated high…

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters.…

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