Tag: NGS

NGS QC Toolkit v2.3.3 – Toolkit for the Quality Control (QC) of Next Generation Sequencing (NGS) data.

NGS QC Toolkit v2.3.3

:: DESCRIPTION

NGS QC Toolkit comprises of user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. It also includes few other tools, which are helpful in NGS data quality control and analysis.

::DEVELOPER

Mukesh Jain (mjain@nipgr.ac.in); Ravi Patel (ravi_patel_4@yahoo.co.in) @ National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 NGS QC Toolkit

:: MORE INFORMATION

Citation

PLoS One. 2012;7(2):e30619. doi: 10.1371/journal.pone.0030619. Epub 2012 Feb 1.
NGS QC Toolkit: a toolkit for quality control of next generation sequencing data.
Patel RK1, Jain M.

ViKNGS v1.0.0 – Variant Integration Kit for NGS

ViKNGS v1.0.0

:: DESCRIPTION

VikNGS is a freely available, user friendly C++ package that uses the RVS methodology to remove the bias in genetic association due to differences in sequencing parameters when combining external NGS data.

::DEVELOPER

Strug lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

ViKNGS

:: MORE INFORMATION

Citation

Baskurt Z, Mastromatteo S, Gong J, Wintle RF, Scherer SW, Strug LJ.
VikNGS: a C++ variant integration kit for next generation sequencing association analysis.
Bioinformatics. 2020 Feb 15;36(4):1283-1285. doi: 10.1093/bioinformatics/btz716. PMID: 31580400; PMCID: PMC7703770.

MetaObtainer – Obtaining the Specified Species from NGS short reads

MetaObtainer

:: DESCRIPTION

MetaObtainer is a tool for obtaining the specified species from next-generation sequencing short reads.

::DEVELOPER

Weihua Pan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MetaObtainer

:: MORE INFORMATION

Citation

Pan W, Chen B, Xu Y.
MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing.
Interdiscip Sci. 2015 Dec;7(4):405-13. doi: 10.1007/s12539-015-0281-x. Epub 2015 Aug 21. PMID: 26293485.

systemPipeR 1.27.27 – NGS Workflow and report Generation Environment

systemPipeR 1.27.27

:: DESCRIPTION

systemPipeR is an R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.

::DEVELOPER

Girke Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

systemPipeR

:: MORE INFORMATION

Citation

H Backman TW, Girke T.
systemPipeR: NGS workflow and report generation environment.
BMC Bioinformatics. 2016 Sep 20;17:388. doi: 10.1186/s12859-016-1241-0. PMID: 27650223; PMCID: PMC5029110.

ExUTR 2017 – Prediction of 3′-UTR Sequences from NGS data

ExUTR 2017

:: DESCRIPTION

ExUTR is a practical and powerful tool that enables rapid genome-wide 3′-UTR prediction from massive RNA-Seq data

::DEVELOPER

ExUTR team,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

ExUTR

:: MORE INFORMATION

Citation

Huang Z, Teeling EC.
ExUTR: a novel pipeline for large-scale prediction of 3′-UTR sequences from NGS data.
BMC Genomics. 2017 Nov 6;18(1):847. doi: 10.1186/s12864-017-4241-1. PMID: 29110697; PMCID: PMC5674806.

ngsTools – Programs to Analyze NGS data for Population Genetics Purposes

ngsTools

:: DESCRIPTION

ngsTools is a collection of programs for population genetics analyses from NGS data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP or genotype calling, and are particularly suitable for low sequencing depth data.

::DEVELOPER

Matteo Fumagalli

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 ngsTools

:: MORE INFORMATION

Citation

ngsTools: methods for population genetics analyses from next-generation sequencing data.
Fumagalli M, Vieira FG, Linderoth T, Nielsen R.
Bioinformatics. 2014 May 15;30(10):1486-7. doi: 10.1093/bioinformatics/btu041.

OncoPaD – Rational Design of Cancer NGS Panels

OncoPaD

:: DESCRIPTION

OncoPaD is a web-tool for the rational design of cancer NGS panels based on mutational data.

::DEVELOPER

 The Biomedical Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

No

:: MORE INFORMATION

Citation

Rubio-Perez C, Deu-Pons J, Tamborero D, Lopez-Bigas N, Gonzalez-Perez A.
Rational design of cancer gene panels with OncoPaD.
Genome Med. 2016 Oct 3;8(1):98. doi: 10.1186/s13073-016-0349-1. PMID: 27716338; PMCID: PMC5047348.

deML v1.1.3 – Maximum Likelihood Demultiplexing for NGS data

deML v1.1.3

:: DESCRIPTION

deML is a program for maximum likelihood demultiplexing of next-generation sequencing data.

::DEVELOPER

Department of Genetics / Bioinformatics Group, Max Planck Institute for Evolutionary Anthropology, Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 deML

:: MORE INFORMATION

Citation

deML: Robust demultiplexing of Illumina sequences using a likelihood-based approach.
Renaud G, Stenzel U, Maricic T, Wiebe V, Kelso J.
Bioinformatics. 2014 Oct 30. pii: btu719.

SNPlice 1.8.0 – Find SNPs influencing splicing in NGS mRNA data

SNPlice 1.8.0

:: DESCRIPTION

SNPlice is a software tool to find and evaluate the co-occurrence of single-nucleotide-polymorphisms (SNP) and altered splicing in next-gen mRNA sequence reads.

::DEVELOPER

The Horvath Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 SNPlice

:: MORE INFORMATION

Citation

SNPlice: Variants that Modulate Intron-retention from RNA-sequencing Data.
Mudvari P, Movassagh M, Kowsari K, Seyfi A, Kokkinaki M, Edwards NJ, Golestaneh N, Horvath A.
Bioinformatics. 2014 Dec 6. pii: btu804

HPG Aligner 2.0.1 – NGS Read Mapping

HPG Aligner 2.0.1

:: DESCRIPTION

HPG Aligner is an ultrafast and highly sensitive Next-Generation Sequencing (NGS) read mapping.

::DEVELOPER

Open source for Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HPG Aligner

:: MORE INFORMATION

Citation

Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.
Tárraga J, Arnau V, Martínez H, Moreno R, Cazorla D, Salavert-Torres J, Blanquer-Espert I, Dopazo J, Medina I.
Bioinformatics. 2014 Aug 20. pii: btu553.

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