FANSe 2 – Fast and Accurate Mapping tool for Nucleotide Sequencing Datasets

FANSe 2

:: DESCRIPTION

FANSe2 is a mapping algorithm which can map a billion reads in hours with ultimate and robust accuracy.

::DEVELOPER

FANSe2 team

:: SCREENSHOTS

FANSe

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 FANSe

:: MORE INFORMATION

Citation

Zhang G *, Fedyunin I, Kirchner S, Xiao C, Valleriani A, Ignatova Z
FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads
Nucl. Acids Res. (2012) 40 (11): e83. doi: 10.1093/nar/gks196

FANSe2: A Robust and Cost-Efficient Alignment Tool for Quantitative Next-Generation Sequencing Applications.
Chuan-Le Xiao, Zhi-Biao Mai, Xin-Lei Lian, Jia-Yong Zhong, Jing-jie Jin, Qing-Yu He *, Gong Zhang *
PLoS One. 2014 Apr 17;9(4):e94250 DOI: 10.1371/journal.pone.0094250

MapSplice 2.1.8 – Mapping of RNA-seq reads for Splice Junction Discovery

MapSplice 2.1.8

:: DESCRIPTION

MapSplice is an algorithm for mapping RNA-seq data to reference genome for splice junction discovery.  MapSplice algorithm to detect splice junctions without any dependence on splice site features. This enables MapSplice to discover non-canonical junctions and other novel splicing events, in additional to the more common canonical junctions.

::DEVELOPER

Bioinformatics Lab @CS.UKy.edu

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 MapSplice

:: MORE INFORMATION

Citation

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery.
Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J.
Nucleic Acids Res, 38(18):e178, 2010.

CompMap – Compressive Short Read Mapping

CompMap

:: DESCRIPTION

CompMap is a reference-based compression program to speed up read mapping to related reference sequences. CompMap is designed to eliminate repeat subsequences based on reference-base compression in the input curating database, which could contain complete genomes, plasmids, and/or other sequences.

::DEVELOPER

Zexuan ZHU

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

  CompMap

:: MORE INFORMATION

Citation:

CompMap: a reference-based compression program to speed up read mapping to related reference sequences.
Zhu Z, Li L, Zhang Y, Yang Y, Yang X.
Bioinformatics. 2014 Oct 4. pii: btu656

BAIT 1.4 – Organizing Genomes and Mapping Rearrangements in Single Cells

BAIT 1.4

:: DESCRIPTION

BAIT (Bioinformatic Analysis of Inherited Templates) is a software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

::DEVELOPER

Terry Fox Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • SAMtools
  • BEDtools
  • R
  • DNAcopy R package
  • gplots R package.

:: DOWNLOAD

 BAIT

:: MORE INFORMATION

Citation

Genome Med. 2013 Sep 13;5(9):82.
BAIT: Organizing genomes and mapping rearrangements in single cells.
Hills M1, O’Neill K, Falconer E, Brinkman R, Lansdorp PM.

BioIDMapper 3.0 – Mapping Biological IDs

BioIDMapper 3.0

:: DESCRIPTION

BioIDMapper is a Cross-referencing and Managing Platform for Biological IDs in R.

:: DEVELOPER

Dr. Xiaoyong Sun, Genomics and Bioinformatics Laboratory

:: SCREENSHOTS

BioIDMapper

:: REQUIREMENTS

  • Linux / WIndows
  • R

:: DOWNLOAD

 BioIDMapper

:: MORE INFORMATION

Citation

Xiaoyong Sun, Michael Lawrence, Zhaoquan Liu, Zhongxu Sun.
BioIDMapper: a Cross-referencing and Managing Platform for Biological IDs in R.
the 3rd International Conference on BioMedical Engineering and Informatics (BMEI 2010). Oct 16-18, 2010. Yantai, China.

HAPAL – Mapping HAPlotype-haplotype Interactions with Adaptive Lasso

HAPAL

:: DESCRIPTION

HAPAL is an R code for mapping HAPlotype-haplotype interactions with Adaptive Lasso

::DEVELOPER

Yuehua Cui, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 HAPAL

:: MORE INFORMATION

Citation:

BMC Genet. 2010 Aug 27;11:79. doi: 10.1186/1471-2156-11-79.
Mapping haplotype-haplotype interactions with adaptive LASSO.
Li M, Romero R, Fu WJ, Cui Y.

iQTL-VC – iQTL mapping with Variance Component mode

iQTL-VC

:: DESCRIPTION

iQTL-VC is an R code for iQTL mapping with Variance Component model in experimental cross.

::DEVELOPER

Yuehua Cui, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 iQTL-VC

:: MORE INFORMATION

Citation:

Li, G.X. and Y.H. Cui. (2010)
A general statistical framework for dissecting parent-of-origin effects underlying triploid endosperm traits in flowering plants.
Annals of Applied Statistics 4(3): 1214-1233.

QTL-GPR – QTL Mapping with Count Trait

QTL-GPR

:: DESCRIPTION

QTL-GPR (quantitative trait loci – Generalized Poisson Regression) is a Matlab code for QTL mapping with count trait.

::DEVELOPER

Yuehua Cui, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • MatLab

:: DOWNLOAD

 QTL-GPR

:: MORE INFORMATION

Citation:

Genetics. 2006 Dec;174(4):2159-72. Epub 2006 Oct 8.
On the generalized poisson regression mixture model for mapping quantitative trait loci with count data.
Cui Y1, Kim DY, Zhu J.

MetaMapp – Mapping and Visualizing Metabolomic data

MetaMapp

:: DESCRIPTION

MetaMapp is a tool to construct metabolomics network graphs from the chemical similarity and mass spectral similarity matrices and the KEGG reaction pair database.

::DEVELOPER

The Fiehn laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 May 16;13:99.
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity.
Barupal DK, Haldiya PK, Wohlgemuth G, Kind T, Kothari SL, Pinkerton KE, Fiehn O.

GPU-BSM 2.7.1 – BS-treated Reads Mapping Tool

GPU-BSM 2.7.1

:: DESCRIPTION

GPU-BSM (GPU-BiSulfite reads Mapping) is a GPU-based tool devised to map bisulfite-treated reads.

::DEVELOPER

the National Institute of Biomedical Technologies, The National Research Council (CNR) , Italy

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CUDA (release ≥6.0).

:: DOWNLOAD

 GPU-BSM

:: MORE INFORMATION

Citation

PLoS One. 2014 May 19;9(5):e97277. doi: 10.1371/journal.pone.0097277. eCollection 2014.
GPU-BSM: a GPU-based tool to map bisulfite-treated reads.
Manconi A, Orro A, Manca E, Armano G, Milanesi L