Tag: High Throughput

BatchPrimer3 1.0 – High Throughput Web Application for PCR and Sequencing Primer Design

BatchPrimer3 1.0

:: DESCRIPTION

BatchPrimer3 is a comprehensive web primer design program using Primer3 core program as a major primer design engine to design different types of PCR primers and sequencing primers in a high-through manner. BatchPrimer3 allows users to design several types of primers including generic primers, hybridization oligos, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. A batch input of large number of sequences and a tab-delimited result output greatly facilitates rapid primer design and ordering process.

::DEVELOPER

Department of Plant Sciences, University of California

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

BatchPrimer3: a high throughput web application for PCR and sequencing primer design.
You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD.
BMC Bioinformatics. 2008 May 29;9:253.

DatasetAssess – Estimate Error Rates in High-throughput Protein Interaction datasets

DatasetAssess

:: DESCRIPTION

 DatasetAssess is a tool to estimate error rates in high-throughput protein interaction datasets and other functional genomic data.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 DatasetAssess

:: MORE INFORMATION

Citation:

Gilchrist, M.A., Salter, L.A., Wagner, A. (2004)
A statistical framework for combining and interpreting proteomic datasets.
Bioinformatics 20, 689-700

TimeLapseAnalyzer 1.34 – High Throughput data processing for Live Cell Imaging

TimeLapseAnalyzer 1.34

:: DESCRIPTION

Time Lapse Analyser (TLA) is a free, cross-platform, open source software for high throughput time-lapse data processing for live cell imaging.

::DEVELOPER

TimeLapseAnalyzer team

:: SCREENSHOTS

TimeLapseAnalyzer

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • MatLab
:: DOWNLOAD

 TimeLapseAnalyzer

:: MORE INFORMATION

Citation

Comput Methods Programs Biomed. 2011 Nov;104(2):227-34. doi: 10.1016/j.cmpb.2011.06.002. Epub 2011 Jun 25.
TimeLapseAnalyzer: multi-target analysis for live-cell imaging and time-lapse microscopy.
Huth J, Buchholz M, Kraus JM, M?lhave K, Gradinaru C, v Wichert G, Gress TM, Neumann H, Kestler HA.

Y-LineageTracker – High-throughput analysis framework for Y-chromosomal Next-generation sequencing data

Y-LineageTracker

:: DESCRIPTION

Y-LineageTracker provides a framework to fully analyze human Y-chromosome sequencing data. Y-LineageTracker supports most of analyses of Y-chromosome sequencing data and facilitates subsequent studies of NRY haplogroups and Y-STRs.

::DEVELOPER

Population Genomics Group (PGG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Y-LineageTracker

:: MORE INFORMATION

Citation

Chen H, Lu Y, Lu D, Xu S.
Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data.
BMC Bioinformatics. 2021 Mar 9;22(1):114. doi: 10.1186/s12859-021-04057-z. PMID: 33750289; PMCID: PMC7941695.

HRIBO 1.5.1 – High-throughput Annotation by Ribo-seq

HRIBO 1.5.1

:: DESCRIPTION

HRIBO is a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing steps and quality control. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary prokaryotic-focused tools, and integrates them with additional computed features. This facilitates both the rapid discovery of ORFs and their prioritization for functional characterization.

::DEVELOPER

HRIBO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Conda

:: DOWNLOAD

HRIBO

:: MORE INFORMATION

Citation

Gelhausen R, Svensson SL, Froschauer K, Heyl F, Hadjeras L, Sharma CM, Eggenhofer F, Backofen R.
HRIBO: high-throughput analysis of bacterial ribosome profiling data.
Bioinformatics. 2021 Aug 4;37(14):2061-2063. doi: 10.1093/bioinformatics/btaa959. Erratum in: Bioinformatics. 2021 Jul 16;: PMID: 33175953; PMCID: PMC8337001.

MUMmerGPU 2.0 – High-throughput sequence alignment using GPU

MUMmerGPU 2.0

:: DESCRIPTION

MUMmerGPU is an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs) in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA) from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies.

::DEVELOPER

Michael Schatz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • nVidia Card

:: DOWNLOAD

MUMmerGPU

:: MORE INFORMATION

MUMmerGPU is an open source project.

Citation:

Cole Trapnell and Michael C. Schatz
Optimizing data intensive GPGPU computations for DNA sequence alignment
Parallel Computing 2009 35(8-9)429-440

Pyicoteo 2.0.7 – Analysis of High-throughput Sequencing data

Pyicoteo 2.0.7

:: DESCRIPTION

Pyicoteo is a suite of tools for the analysis of high-throughput sequencing data. It works with genomic coordinates, it was mainly developed using Solexa/Illumina mapped reads, but in its core it is platform-agnostic.

::DEVELOPER

Eyras Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 Pyicoteo

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Dec 15;27(24):3333-40. Epub 2011 Oct 12.
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.
Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E.

CHASM 3.0 / CHASMplus 1.0 – Cancer-specific High-throughput Annotation of Somatic Mutations

CHASM 3.0 / CHASMplus 1.0

:: DESCRIPTION

CHASM is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage.

CHASMplus is a machine learning method that accurately distinguishes between driver and passenger missense mutations, even for those found at low frequencies or are cancer type-specific.

::DEVELOPER

Karchin Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • MySQL Server
  • Python module MySQLdb

:: DOWNLOAD

CHASMplus

:: MORE INFORMATION

Citation

Tokheim C, Karchin R.
CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers.
Cell Syst. 2019 Jul 24;9(1):9-23.e8. doi: 10.1016/j.cels.2019.05.005. Epub 2019 Jun 12. PMID: 31202631; PMCID: PMC6857794.

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.
Wong WC, Kim D, Carter H, Diekhans M, Ryan MC, Karchin R.
Bioinformatics. 2011 Aug 1;27(15):2147-8. doi: 10.1093/bioinformatics/btr357. Epub 2011 Jun 17.

TreqCG 0.3 – Clustering Accelerates High-Throughput Sequencing Read Mapping

TreqCG 0.3

:: DESCRIPTION

TreqCG is a method to accelerate and improve read mapping based on an initial clustering of up to billions of high-throughput sequencing reads yielding clusters of high stringency and a high degree of overlap.

::DEVELOPER

Schliep lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 TreqCG

:: MORE INFORMATION

Citation

Mahmud, Md and Schliep, Alexander.
TreQ-CG: Clustering Accelerates High-Throughput Sequencing Read Mapping (2014)

GIPro 1.0 – Visualization of High-throughput Genetic and Physical Interaction data

GIPro 1.0

:: DESCRIPTION

GIPro is a Cytoscape plugin developed to allow integrative analysis and visualization of high-throughput genetic and physical interaction data in the context of protein complexes.

::DEVELOPER

The Wodak Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GIPro

:: MORE INFORMATION