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Translate Illumina Bustard output to a fastq file

Author(s)

Khalid Belkhir


Version

1


Subsections

Tool


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Euler

Assembler

 

EULER-SR is a program for de novo assembly of reads. Contrary to the overlap-layout approach, EULER-SR uses a de Bruijn graph to construct an assembly. The assembly of a genome corresponds to an Eulerian path in the de Bruijn graph. Long (possibly erroneous) reads, and mate-pairs are used to determine parts of the correct Eulerian traversal in the assembly.

Author(s)

Mark Chaisson, Pavel Pevzner, Dumitru Brinza, Haixu Tang, Glenn Tesler


Version

1.1.2


Subsections

Assembler


Tags

De novo


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iRAP is a flexible computational pipeline for RNA-seq that integrates many existing tools for filtering and mapping reads, quantifying expression and testing for differential expression. It is aimed at a broad group of users with basic bioinformatics training and requires little experience with the command line but also provides more advanced users with the ability to customise the options used by their chosen tools.

Author(s)

Unknown


Version

1


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This version processes a de novo assembly to generate a fasta reference file and a gtf file.

iRAP is a flexible computational pipeline for RNA-seq that integrates many existing tools for filtering and mapping reads, quantifying expression and testing for differential expression. It is aimed at a broad group of users with basic bioinformatics training and requires little experience with the command line but also provides more advanced users with the ability to customise the options used by their chosen tools.

Author(s)

Unknown


Version

1


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Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

Author(s)

Unknown


Version

1.1


Subsections

Tool - Blast


Tags

RNA-seq - Apps


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Megablast

Alignment

 

Mega BLAST uses a greedy algorithm [1] for the nucleotide sequence alignment search. This program is optimized for aligning sequences that differ slightly as a result of sequencing or other similar "errors". When larger word size is used (see explanation below), it is up to 10 times faster than more common sequence similarity programs. Mega BLAST is also able to efficiently handle much longer DNA sequences than the blastn program of traditional BLAST algorithm.

Author(s)

NCBI -Tao Tao


Version

1


Subsections

Alignment - Blast


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Build database giving a sequence file in order to blast query sequences on it using magablast. Treatment performed using formatDB and megablast (8 cores).

Author(s)

Altschul, Madden, Schaeffer, Zhang, Miller, Lipman ... [wrapper : MBB development team]


Version

1


Subsections

Blast


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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


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Reciprocal Best Hit

Author(s)

Wrapper by MBB Development team


Version

1


Subsections

Blast


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wgsim simulator program from samtools

Author(s)

Heng Li


Version

1


Subsections

Tool - Mapping


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Base composition and read size distribution

Author(s)

MBB dev team


Version

1


Subsections

Tool


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ReadSeq

Tool

 

Readseq was written originally around 1989 a component of a sequence analysis program, but when I added a small, simple command-line interface, it took on a life of its own as a conversion program for bioinformatics. It's main contribution to bioinformatics is it takes on the job of guessing what your input biosequence data format is, and converting it to what your software knows how to handle.

Author(s)

D. Gilbert


Version

1


Subsections

Tool


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Under development

Author(s)

MBB Development team


Version

1


Subsections

Tool


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MBB version of SeqClean (used to remove adaptators)

Author(s)

The Institute for Genomic Research - Geo Pertea


Version

1


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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


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