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.

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.

PurityEst – Estimating Purity of Human Tumor Samples using Next-generation Sequencing Data

PurityEst

:: DESCRIPTION

PurityEst is a novel algorithm which infers the tumor purity level from the allelic differential representation of heterozygous loci with somatic mutations in a human tumor sample with a matched normal tissue using next-generation sequencing data.

::DEVELOPER

Xiaoping Su

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 PurityEst

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2265-6. doi: 10.1093/bioinformatics/bts365.
PurityEst: estimating purity of human tumor samples using next-generation sequencing data.
Su X, Zhang L, Zhang J, Meric-Bernstam F, Weinstein JN.

VirusSeq – Detecting Known Viruses and their integration Sites using Next-generation Sequencing of Human Cancer Tissue

VirusSeq

:: DESCRIPTION

VirusSeq is a software for detecting known viruses and their integration sites in the human genome using next-generation sequencing data.

::DEVELOPER

Xiaoping Su

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 VirusSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 15;29(2):266-7. doi: 10.1093/bioinformatics/bts665.
VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue.
Chen Y, Yao H, Thompson EJ, Tannir NM, Weinstein JN, Su X.

CONSERTING – Copy Number Segmentation by Regression Tree in Next Generation Sequencing

CONSERTING

:: DESCRIPTION

CONSERTING (Copy Number Segmentation by Regression Tree in Next Generation Sequencing) is an accurate method for detecting somatic DNA copy number variation in whole genome sequencing data.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R package

:: DOWNLOAD

 CONSERTING

:: MORE INFORMATION

SequencEnG – Learning Resource for Next-generation Sequencing (NGS) Techniques

SequencEnG

:: DESCRIPTION

SequencEnG (Sequencing Techniques Engine for Genomics) is an educational resource for interactive learning of next-generation sequencing (NGS) techniques.

::DEVELOPER

Jun S. Song’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

SequencEnG

:: MORE INFORMATION

Citation

Zhang Y, Manjunath M, Kim Y, Heintz J, Song JS.
SequencEnG: an interactive knowledge base of sequencing techniques.
Bioinformatics. 2019 Apr 15;35(8):1438-1440. doi: 10.1093/bioinformatics/bty794. PMID: 30202870; PMCID: PMC6478014.

SNVMix2 – Detect Single Nucleotide Variants from Next Generation Sequencing

SNVMix2

:: DESCRIPTION

SNVMix is designed to detect single nucleotide variants from next generation sequencing data. SNVMix is a post-alignment tool. Given a pileup file (either Maq or Samtools format) as input and model parameters, SNVMix will output the probability that each position is one of three genotypes:  aa (homozygous for the reference allele, where the reference is the genome the reads were aligned to), ab (heterozygous) and bb (homozygous for a non-reference allele).  A tool for fitting the model using expectation maximization is also supplied (use -T option).

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SNVMix

:: MORE INFORMATION

Citation

Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.
Bioinformatics. 2010 Mar 15;26(6):730-6.

GAM-NGS 1.1b – Genome Assemblies Merger for Next Generation Sequencing

GAM-NGS 1.1b

:: DESCRIPTION

GAM-NGS is able to merge two or more assemblies and it rteturns an improved assembly (more contiguous and more correct). GAM-NGS shows its full potential with multi-library Illumina-based projects.

::DEVELOPER

GAM-NGS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GAM-NGS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 7:S6. doi: 10.1186/1471-2105-14-S7-S6. Epub 2013 Apr 22.
GAM-NGS: genomic assemblies merger for next generation sequencing.
Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A.

TagDust 2.33 – Extracts Mappable Reads from NGS gata.

TagDust 2.33

:: DESCRIPTION

TagDust is a program to eliminate artifactual reads from next-generation sequencing data sets.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TagDust

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 Jan 28;16(1):24.
TagDust2: a generic method to extract reads from sequencing data.
Lassmann T

Lassmann T., et al. (2009)
TagDust – A program to eliminate artifacts from next generation sequencing data.
Bioinformatics. 2009 November 1; 25(21): 2839–2840.

SAMStat 1.5.1 – Display Sequence Statistics for Next Generation Sequencing

SAMStat 1.5.1

:: DESCRIPTION

SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SAMStat

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 1;27(1):130-1. doi: 10.1093/bioinformatics/btq614. Epub 2010 Nov 18.
SAMStat: monitoring biases in next generation sequencing data.
Lassmann T1, Hayashizaki Y, Daub CO.