ChiTaH – Chimeric Transcripts from High-throughput sequencing data

ChiTaH

:: DESCRIPTION

ChiTaH is a fast and accurate tool for identifying known human chimeric sequences from high-throughput sequencing data.

::DEVELOPER

Rajesh Detroja

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ChiTaH

:: MORE INFORMATION

Citation

Detroja R, Gorohovski A, Giwa O, Baum G, Frenkel-Morgenstern M.
ChiTaH: a fast and accurate tool for identifying known human chimeric sequences from high-throughput sequencing data.
NAR Genom Bioinform. 2021 Nov 26;3(4):lqab112. doi: 10.1093/nargab/lqab112. PMID: 34859212; PMCID: PMC8633610.

STARRInIGHTS – Strain-based Tree Analysis and Recombinant Region Inference In Genomes from High-Throughput Sequencing projects

STARRInIGHTS

:: DESCRIPTION

STARRInIGHTS is a computational pipeline for inferring homologous recombination breakpoints in populations of closely related bacterial genomes.

::DEVELOPER

The Alm lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX
Perl
Java

:: DOWNLOAD

STARRInIGHTS

:: MORE INFORMATION

GenOO 1.5.1 – A Modern Perl Framework for High Throughput Sequencing analysis

GenOO 1.5.1

:: DESCRIPTION

GenOO is an open-source; object-oriented Perl framework specifically developed for the design of High Throughput Sequencing (HTS) analysis tools.

::DEVELOPER

Z. MOURELATOS LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

GenOO

:: MORE INFORMATION

Citation

GenOO: A programming framework for High Throughput Sequencing analysis
Manolis Maragkakis, Panagiotis Alexiou, Zissimos Mourelatos
doi: https://doi.org/10.1101/019265

VNTRseek 1.08 – Detect Tandem Repeat Variants in High-throughput Sequencing data

VNTRseek 1.08

:: DESCRIPTION

VNTRseek is a targeted, effient VNTR (Variable Number of Tandem Repeats) detection software which can provide essential information on VNTR occurrence and characteristics of minisatellites.

::DEVELOPER

Laboratry of Bioinformatcis at Boston University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

VNTRseek

:: MORE INFORMATION

Citation

VNTRseek-a computational tool to detect tandem repeat variants in high-throughput sequencing data.
Gelfand Y, Hernandez Y, Loving J, Benson G.
Nucleic Acids Res. 2014 Jul 23. pii: gku642.

HTSCluster 2.0.8 – Clustering High Throughput Sequencing (HTS) data

HTSCluster 2.0.8

:: DESCRIPTION

HTSCluster implements a Poisson mixture model to cluster observations (e.g., genes) in high throughput sequencing data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).

::DEVELOPER

Andrea Rau <andrea.rau at jouy.inra.fr>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
R

:: DOWNLOAD

HTSCluster

:: MORE INFORMATION

Citation:

Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models.
Rau A, Maugis-Rabusseau C, Martin-Magniette ML, Celeux G.
Bioinformatics. 2015 Jan 5. pii: btu845.

mirTools 2.0 – non-coding RNA Discovery, Profiling and Functional Annotation based on High-throughput Sequencing

mirTools 2.0

:: DESCRIPTION

mirTools was developed to allow researchers to comprehensively characterize small RNA transcriptome.

::DEVELOPER

mirTools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

mirTools

:: MORE INFORMATION

Citation

Zhu EL, Zhao FQ, Zhou LL, Hou HB, Xu G, Li XK, Bao QY, Sun ZS and Wu JY.
mirTools: microRNA profiling and discovery based on high-throughput sequencing.
Nucl. Acids Res. (2010) 38 (suppl 2): W392-W397.

Tn-seq Explorer 1.5B – Analysis of High-throughput Sequencing data of Transposon Mutant Libraries

Tn-seq Explorer 1.5B

:: DESCRIPTION

Tn-seq Explorer allows users to explore and analyze Tn-seq data for prokaryotic (bacterial or archaeal) genomes.

::DEVELOPER

Computational Microbiology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows
JAVA

:: DOWNLOAD

Tn-seq Explorer

:: MORE INFORMATION

Citation

Tn-seq explorer: a tool for analysis of high-throughput sequencing data of transposon mutant libraries.
Solaimanpour S, Sarmiento F, Mrázek J.
PLoS One. 2015 May 4;10(5):e0126070. doi: 10.1371/journal.pone.0126070

Cypiripi – Exact Genotyping of CYP2D6 using High-throughput Sequencing data

Cypiripi

:: DESCRIPTION

Cypiripi is a tool for exact genotyping of CYP2D6 using High Throughput Sequencing Data.

::DEVELOPER

Lab for Computational Biology at SFU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

Cypiripi

:: MORE INFORMATION

Citation

Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data.
Numanagić I, Malikić S, Pratt VM, Skaar TC, Flockhart DA, Sahinalp SC.
Bioinformatics. 2015 Jun 15;31(12):i27-i34. doi: 10.1093/bioinformatics/btv232.

segmentSeq 2.26.0 – Identifying small RNA loci from High-throughput Sequencing data

segmentSeq 2.26.0

:: DESCRIPTION

segmentSeq is a methods for identifying small RNA loci from high-throughput sequencing data

::DEVELOPER

Thomas J. Hardcastle

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
R package
Bioconductor

:: DOWNLOAD

segmentSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 15;28(4):457-63. doi: 10.1093/bioinformatics/btr687. Epub 2011 Dec 9.
Identifying small interfering RNA loci from high-throughput sequencing data.
Hardcastle TJ, Kelly KA, Baulcombe DC.

SEQBIAS 1.40.0 – Estimation of Per-position Bias in High-throughput Sequencing data

SEQBIAS 1.40.0

:: DESCRIPTION

SEQBIAS implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.

::DEVELOPER

Daniel C. Jones

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ WIndows/MacOsX
R package
BioConductor

:: DOWNLOAD

SEQBIAS

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Apr 1;28(7):921-8. doi: 10.1093/bioinformatics/bts055. Epub 2012 Jan 28.
A new approach to bias correction in RNA-Seq.
Jones DC, Ruzzo WL, Peng X, Katze MG.