Online tools NGS

Online Tools

Expand all - Reduce all Items : 11 / 41

Number of results per page

Reciprocal Best Hit

Author(s)

Wrapper by MBB Development team


Version

1


Subsections

Blast


Sorry restricted access... How to access this tool ?

wgsim simulator program from samtools

Author(s)

Heng Li


Version

1


Subsections

Tool - Mapping


Sorry restricted access... How to access this tool ?

Base composition and read size distribution

Author(s)

MBB dev team


Version

1


Subsections

Tool


Sorry restricted access... How to access this tool ?

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


Sorry restricted access... How to access this tool ?

Under development

Author(s)

MBB Development team


Version

1


Subsections

Tool


Sorry restricted access... How to access this tool ?

MBB version of SeqClean (used to remove adaptators)

Author(s)

The Institute for Genomic Research - Geo Pertea


Version

1


Sorry restricted access... How to access this tool ?

This tool is a wrapper around NCBI blast.
It allows users to blast their sequences on NCBI nr database or on a their own database that will be cretaed from an uploded fasta file.

Author(s)

BELKHIR


Version

1


Sorry restricted access... How to access this tool ?

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


Sorry restricted access... How to access this tool ?

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


Sorry restricted access... How to access this tool ?

VCFanlyser

Mapping

 

This tool is aimed at helping to analyse a small to medium vcf files of genotyped individuals from one or more populations.
Descriptive statistics (Pi, MAF spectrum, F, IBS …) , multivariate analysis (PCA and t-SNE) and population structuration (Fst and fastStructure) can be calculated after filtering snps for min MAF and max missing values.

Author(s)

BELKHIR


Version

1


Subsections

Mapping


Velvet

Assembler

 

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

Author(s)

Daniel Zerbino and Ewan Birney


Version

0.7


Subsections

Assembler


Tags

De novo


Sorry restricted access... How to access this tool ?