Tag: MAPper

GNUMAP 3.0.2 – Genomic Next-generation Universal MAPper

GNUMAP 3.0.2

:: DESCRIPTION

The GNUMAP (Genomic Next-generation Universal MAPper) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. Currently, gnumap is designed to be used with the _int.txt data received from the Solexa/Illumina machine.

::DEVELOPER

GNUMAP Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GNUMAP

:: MORE INFORMATION

Citation:

Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns BR, Johnson WE
The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing
Bioinformatics (2010) 26 (1): 38-45.

FlaiMapper 3.0.0 – Fragment Location Annotation Identification Mapper

FlaiMapper 3.0.0

:: DESCRIPTION

FlaiMapper is a method that extracts and annotates the locations of sncRNA-derived RNAs (sncdRNAs).

::DEVELOPER

FlaiMapper team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FlaiMapper

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 22. pii: btu696.
FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data.
Hoogstrate Y, Jenster G, Martens-Uzunova ES

FastQTL 2.184 – Fast and Efficient QTL mapper for thousands of Molecular Phenotypes

FastQTL 2.184

:: DESCRIPTION

FastQTL is a method that implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool.

::DEVELOPER

FunPopGen lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 FastQTL

:: MORE INFORMATION

Citation

Fast and efficient QTL mapper for thousands of molecular phenotypes.
Ongen H, Buil A, Brown AA, Dermitzakis ET, Delaneau O.
Bioinformatics. 2015 Dec 26. pii: btv722.

CoVaMa 0.7 – Co-Variation Mapper for Disequilibrium Analysis of Mutant Loci

CoVaMa 0.7

:: DESCRIPTION

CoVaMa detects correlated patterns of mutations in a viral quasi-species. CoVaMa takes NGS alignment data (SAM) and populates large matrices of contingency tables that correspond to every possible pairwise interaction of nucleotides or amino acids in the viral genome.

::DEVELOPER

CoVaMa team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

 CoVaMa

:: MORE INFORMATION

Citation

CoVaMa: Co-Variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data.
Routh A, Chang MW, Okulicz JF, Johnson JE, Torbett BE.
Methods. 2015 Sep 22. pii: S1046-2023(15)30105-5. doi: 10.1016/j.ymeth.2015.09.021.

PRISM 1.1.6 / PRISM_CTX 1.0.1 – Pair Read Informed Split Mapper

PRISM 1.1.6 / PRISM_CTX 1.0.1

:: DESCRIPTION

PRISM is a software for split read (reads which span across a structrual variant — SV ) mapping and SV calling from the mapping result. PRISM is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs.

PRISM_CTX is a tool for detecting inter-chromosome trans-location events.

::DEVELOPER

Computational Biology Lab, University of Toronto

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 PRISM / PRISM_CTX

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Oct 15;28(20):2576-83. doi: 10.1093/bioinformatics/bts484. Epub 2012 Jul 31.
PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants.
Jiang Y1, Wang Y, Brudno M.

BatMeth 1.04b – Improved Mapper for Bisulfite Sequencing Reads on DNA Methylation

BatMeth 1.04b

:: DESCRIPTION

BatMeth is an algorithm that integrates novel mismatch counting, list filtering, mismatch stage filtering and fast mapping onto two indexes to improve unique mapping rate, speed and precision.

::DEVELOPER

Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BatMeth

:: MORE INFORMATION

Citation

Genome Biol. 2012 Oct 3;13(10):R82. [Epub ahead of print]
BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation.
Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y, Wei CL, Sung WK.

RUM 2.0.5_06 – Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper

RUM 2.0.5_06

:: DESCRIPTION

RUM (RNA-Seq Unified Mapper)  is an alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.

::DEVELOPER

the Computational Biology and Informatics Laboratory at the University of Pennsylvania

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

 RUM

:: 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.

ANFO 0.98 – Mapper for Ancient DNA

ANFO 0.98

:: DESCRIPTION

Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes more after BLAST/BLAT. It’s most useful for the alignment of sequencing reads where the DNA sequence is somehow modified (think ancient DNA or bisulphite treatment) and/or there is more divergence between sample and reference than what fast mappers will handle gracefully (say the reference genome is missing and a related species is used instead).

::DEVELOPER

Udo Stenzel <udo_stenzel@eva.mpg.de> @ Department of Genetics/Bioinformatics – Max Planck Institut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Anfo

:: MORE INFORMATION