mrFAST 2.6.1.0 – Micro Read Fast Alignment Search Tool

mrFAST 2.6.1.0

:: DESCRIPTION

mrFAST is micro-read Fast Alignment Search Tool. It is designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner.

::DEVELOPER

Eichler Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Complier

:: DOWNLOAD

mrFAST

:: MORE INFORMATION

Can Alkan, Jeffrey M Kidd, Tomas Marques-Bonet, Gozde Aksay, Francesca Antonacci, Fereydoun Hormozdiari, Jacob O Kitzman, Carl Baker, Maika Malig, Onur Mutlu, S Cenk Sahinalp, Richard A Gibbs & Evan E Eichler
Personalized copy number and segmental duplication maps using next-generation sequencing
Nature Genetics 41, 1061 – 1067 (2009)

mrsFAST-Ultra 3.4.2 – Micro-read Substitution-only Fast Alignment Search Tool

mrsFAST-Ultra 3.3.8

:: DESCRIPTION

mrsFAST (Micro-read Substitution-only Fast Alignment Search Tool ) is a cache oblivious mapper that is designed to map short reads to reference genome. mrsFAST maps short reads with respect to user defined error threshold. In this manual, we will show how to choose the parameters and tune mrsFAST with respect to the library settings. mrsFAST is designed to find ‘all’ the mappings for a given set of reads

::DEVELOPER

Eichler Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Complier

:: DOWNLOAD

mrsFAST-Ultra

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 May 8.
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.
Hach F1, Sarrafi I, Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC.

Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC. (2010).
mrsFAST: a cache-oblivious algorithm for short-read mapping.
Nat Methods Aug;7(8):576-7.

mrCaNaVaR 0.51 – Micro-read Copy Number Variant Regions

mrCaNaVaR 0.51

:: DESCRIPTION

mrCaNaVaR is a copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.

::DEVELOPER

Can Alkan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX
mrFAST / mrsFAST
C Complier

:: DOWNLOAD

mrCaNaVaR

:: MORE INFORMATION

Citation

Can Alkan, Jeffrey M. Kidd, Tomas Marques-Bonet, Gozde Aksay, Francesca Antonacci, Fereydoun Hormozdiari, Jacob O. Kitzman, Carl Baker, Maika Malig, Onur Mutlu, S. Cenk Sahinalp, Richard A. Gibbs, Evan E. Eichler.
Personalized copy number and segmental duplication maps using next-generation sequencing.
Nature Genetics, Oct, 41(10):1061-1067, 2009.