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

:: 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.

Fixseq – Universal Count Correction for high-throughput Sequencing

Fixseq

:: DESCRIPTION

FIXSEQ is a over-dispersion correction technique that serves as a smarter way to de-duplicate counts.

::DEVELOPER

the Gifford Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • R

:: DOWNLOAD

  Fixseq

:: MORE INFORMATION

Citation

Hashimoto TB, Edwards MD, Gifford DK.
Universal count correction for high-throughput sequencing.
PLoS Comput Biol. 2014 Mar 6;10(3):e1003494. doi: 10.1371/journal.pcbi.1003494. PMID: 24603409; PMCID: PMC3945112.

dd_detection – Detecting Dispersed Duplications in High-Throughput Sequencing Data

dd_detection

:: DESCRIPTION

dd_detection is a tool for finding dispersed duplications (DDs) in high throughput sequencing data.

::DEVELOPER

dd_detection team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • samtools
  • C++ compiler

:: DOWNLOAD

 dd_detection

:: MORE INFORMATION

Citation:

Detecting Dispersed Duplications in High-Throughput Sequencing Data using a Database-Free Approach.
Kroon M, Lameijer EW, Lakenberg N, Hehir-Kwa JY, Thung DT, Slagboom PE, Kok JN, Ye K.
Bioinformatics. 2015 Oct 27. pii: btv621.

bcbio 1.2.8 – Best-practice pipelines for fully automated High Throughput Sequencing analysis

bcbio-nextgen 1.2.8

:: DESCRIPTION

bcbio-nextgen is a python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.

::DEVELOPER

Blue Collar Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 bcbio-nextgen

:: MORE INFORMATION