InteMAP 1.0 – Integrated Metagenomic Assembly pipeline for NGS Short Reads

InteMAP 1.0

:: DESCRIPTION

InteMAP is a pipeline which integrates individual assemblers for assembling metagenomic short sequencing reads.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

  InteMAP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 Aug 7;16:244. doi: 10.1186/s12859-015-0686-x.
InteMAP: Integrated metagenomic assembly pipeline for NGS short reads.
Lai B, Wang F, Wang X, Duan L, Zhu H

SNPGenie – Estimating Evolutionary parameters to Detect Natural Selection using pooled NGS data

SNPGenie

:: DESCRIPTION

SNPGenie is a program to estimate evolutionary parameters from pooled next-generation sequencing (NGS) data.

::DEVELOPER

Chase W. Nelson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 SNPGenie

:: MORE INFORMATION

Citation

SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data.
Nelson CW, Moncla LH, Hughes AL.
Bioinformatics. 2015 Jul 29. pii: btv449.

UNCcombo 0.1 – Likelihood based Association Testing for NGS data without intermediate Genotype Galling

UNCcombo 0.1

:: DESCRIPTION

UNCcombo is a R package to perform single marker association testing on raw next generation sequencing data.

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ MacOsX
  • R

:: DOWNLOAD

 UNCcombo

:: MORE INFORMATION

Citation

Likelihood Based Complex Trait Association Testing for Arbitrary Depth Sequencing Data.
Yan S, Yuan S, Xu Z, Zhang B, Zhang B, Kang G, Byrnes A, Li Y.
Bioinformatics. 2015 May 14. pii: btv307.

Pathoscope 2.0.6 / Clinical PathoScope 1.0.4 – Species Identification and Strain Attribution with Unassembled Sequencing data

Pathoscope 2.0.6  / Clinical PathoScope 1.0.4

:: DESCRIPTION

Pathoscope takes a next-generation sequencing reads from a mixture sample of multiple strains of genomes and it predicts which genomes potentially belongs there. Different from most of approach including composition method or similarity search with a daunting task of de novo assembly, the software applies the propagation of evidence in the Bayesian framework to an initial alignment result and reassign an correct membership of mapping by using the expectation and maximization algorithm.

Clinical Pathoscope is a program to identify pathogens/commensals/contaminants in unassembled sequencing reads.

::DEVELOPER

W. Evan Johnson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Pathoscope / Clinical PathoScope

:: MORE INFORMATION

Citation

PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.
Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA, Johnson WE.
Microbiome. 2014 Sep 5;2:33. doi: 10.1186/2049-2618-2-33.

Genome Res. 2013 Oct;23(10):1721-9. doi: 10.1101/gr.150151.112.
Pathoscope: Species identification and strain attribution with unassembled sequencing data.
Francis OE, Bendall M, Manimaran S, Hong C, Clement NL, Castro-Nallar E, Snell Q, Schaalje GB, Clement MJ, Crandall KA, Johnson WE.

BMC Bioinformatics. 2014 Aug 4;15:262. doi: 10.1186/1471-2105-15-262.
Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data.
Byrd AL, Perez-Rogers JF, Manimaran S, Castro-Nallar E, Toma I, McCaffrey T, Siegel M, Benson G, Crandall KA1, Johnson WE.

JAMM 1.0.7rev3 – Peak Finder for NGS Datasets

JAMM 1.0.7rev3

:: DESCRIPTION

JAMM (Joint Analysis of NGS replicates via Mixture Model clustering)is a peak finder for NGS datasets that can integrate replicates and assign peak boundaries accurately.

::DEVELOPER

JAMM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 JAMM

:: MORE INFORMATION

Citation:

JAMM: A Peak Finder for Joint Analysis of NGS Replicates.
Ibrahim MM, Lacadie SA, Ohler U.
Bioinformatics. 2014 Sep 15. pii: btu568.

Nesoni 0.132 – Swiss Army Knife for NGS SNP calling / RNA-Seq DGE / Read Cleaning

Nesoni 0.132

:: DESCRIPTION

Nesoni is a high-throughput sequencing data analysis toolset, which the VBC has developed to cope with the flood of Illumina, 454, and SOLiD data now being produced.

::DEVELOPER

Victorian Bioinformatics Consortium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 Nesoni

:: MORE INFORMATION

MAPseeker 2.0 – Analysis and Visualization of Multiplexed Accessibility Probing read out through NGS

MAPseeker 2.0

:: DESCRIPTION

MAPseeker is a software for rapid analysis and visualization of Multiplexed Accessibility Probing read out through Next Generation Sequencing (MAP-seq) data.

::DEVELOPER

Das Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX/ Windows
  • MatLab

:: DOWNLOAD

 MAPseeker

 :: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1086:95-117. doi: 10.1007/978-1-62703-667-2_6.
Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol.
Seetin MG1, Kladwang W, Bida JP, Das R.

mirTrios – Detection of de novo and rare inherited Mutations from Trios-based NGS

mirTrios

:: DESCRIPTION

mirTrios was developed for identification and comprehensive analysis the de novo and rare inherited variants with one or multiple trios samples based on high-throughput sequencing data starting from a VCF file (version 4). It uses reference gene definitions and hg19 genomic coordinates for annotation.

::DEVELOPER

mirTrios team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JDK

:: DOWNLOAD

 mirTrios

:: MORE INFORMATION

Citation

mirTrios: an integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing.
Li J, Jiang Y, Wang T, Chen H, Xie Q, Shao Q, Ran X, Xia K, Sun ZS, Wu J.
J Med Genet. 2015 Apr;52(4):275-81. doi: 10.1136/jmedgenet-2014-102656.

NGS-MC – Markovian Inference for Molecular Sequences Using NGS Data

NGS-MC

:: DESCRIPTION

NGS-MC is an R package which calculates the statistics and estimators in a Markov sequence model including the effective coverage, a chi-square statistic for k-words, normal approximation for every k-word, and five estimators for the order of Markov chain from NGS short read data.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

 NGS-MC

:: MORE INFORMATION

Citation

Jie Ren, Kai Song, Minghua Deng, Gesine Reinert, Charles H. Cannon, Fengzhu Sun (2015),
Inference of Markovian Properties of Molecular Sequences from NGS Data and Applications to Comparative Genomics.
Bioinformatics. 2015 Jun 30. pii: btv395.

NGS-Logistics – Federated Analysis of NGS Sequence Variants across multiple Locations

NGS-Logistics

:: DESCRIPTION

NGS-Logistics is a methodology for federated analysis of sequence variants from personal genomes.

::DEVELOPER

NGS-Logistics team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NGS-Logistics: federated analysis of NGS sequence variants across multiple locations.
Ardeshirdavani A, Souche E, Dehaspe L, Van Houdt J, Vermeesch JR, Moreau Y.
Genome Med. 2014 Sep 17;6(9):71. doi: 10.1186/s13073-014-0071-9.