LRCstats – Evaluating Long Reads Correction tools

LRCstats

:: DESCRIPTION

LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

LRCstats

:: MORE INFORMATION

Citation

La S, Haghshenas E, Chauve C.
LRCstats, a tool for evaluating long reads correction methods.
Bioinformatics. 2017 Nov 15;33(22):3652-3654. doi: 10.1093/bioinformatics/btx489. PMID: 29036421.

STEPP 1.0 – SVM Technique for Evaluating Proteotypic Peptides

STEPP 1.0

:: DESCRIPTION

STEPP is a support vector machine (SVM) model that uses a simple descriptor space based on 35 properties of amino acid content, charge, hydrophilicity and polarity for the quantitative prediction of proteotypic peptides.

::DEVELOPER

Computational Biology & Bioinformatics, Pacific Northwest National Laboratory

:: SCREENSHOTS

STEPP

:: REQUIREMENTS

  • Windows/ MacOsX
  • JAVA 

:: DOWNLOAD

 STEPP

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jul 1;26(13):1677-83.
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics.
Webb-Robertson BJ, Cannon WR, Oehmen CS, Shah AR, Gurumoorthi V, Lipton MS, Waters KM.

BEERS – Benchmarker for Evaluating the Effectiveness of RNA-Seq Software

BEERS

:: DESCRIPTION

BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data

::DEVELOPER

the Computational Biology and Informatics Laboratory (in the Center for Bioinformatics at the University of Pennsylvania)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

 BEERS

:: MORE INFORMATION

Citation:

Gregory R. Grant, Michael H. Farkas, Angel Pizarro, Nicholas Lahens, Jonathan Schug, Brian Brunk, Christian J. Stoeckert Jr, John B. Hogenesch and Eric A. Pierce.
Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper (RUM) 
Bioinformatics. 2011 Sep 15;27(18):2518-28. Epub 2011 Jul 19.