Online tools

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Query : Mapping [subsection]

Online Tools (7)

Bowtie

Mapping

 

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

Author(s)

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast


Version

0.12.5


Subsections

Mapping


PASS

Mapping

 

PASS has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by Solexa, SOLiD and Roche-454 technology. The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is performed by dynamic programming. Pass is useful for single read mapping, paired-end resequensing, small RNA discovery and RNA-seq mapping.

Author(s)

Campagna et al


Version

1.2


Subsections

Mapping


Soap2

Mapping

 

SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another remarkable improvement of SOAPaligner is that it now supports a wide range of the read length. SOAPaligner benefitted in time and space efficiency by a revolution in the basic data structures and algorithms used.The core algorithms and the indexing data structures (2way-BWT) are developed by the algorithms research group of the Department of Computer Science, the University of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).

Author(s)

T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu


Version

2.20


Subsections

Mapping


BWA Sampe

Mapping

 

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. Please see the BWA manual page for more information.

Author(s)

Heng Li, Chi-Kwong Wong


Version

0.5.8


Subsections

Mapping - Assembler


Tags

bwa


BWA Samse

Assembler

 

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. Please see the BWA manual page for more information.

Author(s)

Heng Li, Chi-Kwong Wong


Version

0.5.8


Subsections

Assembler - Mapping


Tags

bwa


TopHat

Mapping

 

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

Author(s)

CBCB


Version

1.3.0


Subsections

Mapping


Tags

RNA-seq


wgsim simulator program from samtools

Author(s)

Heng Li


Version

1


Subsections

Tool - Mapping


Softwares (3)

PopPhyl

Tool

  

The PopPhyl project provides a set of publicly available tools C++ code to achieve SNP and genotype calling (with home made algorithms). Also are provided wrappers to use this tools in the Galaxy platforms.

Executables tools

  • Reads2SNP C++ executable (Static compilation for 32, 64 bits Linux and binary for MacOS)(download)
  • dNdSpiNpiS C++ executable (Static compilation for 64 bits Linux)(download)
  • ORF extractor perl script (download)
Galaxy-related tools

Author(s)

Nicolas Galtier et al.


Version

1


Platform

Linux - Windows - Mac


Source

Yes


Downloads

0


Subsections

Tool - Mapping - Assembler


Tags

ISEM




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