LIQA – Long-read Isoform Quantification and Analysis

LIQA

:: DESCRIPTION

LIQA (Long-read Isoform Quantification and Analysis) is an Expectation-Maximization based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read RNA-seq data. LIQA incorporates base-pair quality score and isoform-specific read length information to assign different weights across reads instead of summarizing isoform-specific read counts directly. Moreover, LIQA can detect DAS events between conditions using isoform usage estimates.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Pyton

:: DOWNLOAD

LIQA

:: MORE INFORMATION

Citation

Yu Hu, Li Fang, Xuelian Chen, Jiang F. Zhong, Mingyao Li, Kai Wang.
LIQA: Long-read Isoform Quantification and Analysis.
2020. bioRxiv doi: https://doi.org/10.1101/2020.09.09.289793

krocus 0.0.15 – Predict MLST directly from uncorrected long reads

krocus 0.0.15

:: DESCRIPTION

Krocus can predict a ST directly from uncorrected long reads, and which was designed to consume read data as it is produced, providing results in minutes.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Krocus

:: MORE INFORMATION

Citation

PeerJ. 2018 Jul 31;6:e5233. doi: 10.7717/peerj.5233. eCollection 2018.
Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus.
Page AJ, Keane JA.

AGILE 0.4.0 – AliGnIng Long rEads

AGILE 0.4.0

:: DESCRIPTION

AGILE is a sequence mapping tool specifically designed to map the longer reads (read length > 200) to a given reference genome. Currently it works for 454 reads, but efforts are being made to make it suitable to work for all sequencers, which produce longer reads. Looking at the current trend of increasing read lengths, soon most of the sequencers have read lengths > 200.

::DEVELOPER

Sanchit Misra

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

AGILE

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 15;27(2):189-95. Epub 2010 Nov 18.
Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.
Misra S, Agrawal A, Liao WK, Choudhary A.