Tag: NGS data

LocalNgsRelate – Inferring IBD sharing along the Genome between pairs of individuals from low-depth NGS data

LocalNgsRelate

:: DESCRIPTION

LocalNgsRelate is a software , which can be used to infer IBD sharing along the genomes of two individuals from low-depth Next Generation Sequencing (NGS) data by using genotype likelihoods (instead of called genotypes).

::DEVELOPER

LocalNgsRelate team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

LocalNgsRelate

:: MORE INFORMATION

Citation

Severson AL, Korneliussen TS, Moltke I.
LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data.
Bioinformatics. 2021 Oct 28:btab732. doi: 10.1093/bioinformatics/btab732. Epub ahead of print. PMID: 34718411.

MitoScape v1.0 – Machine-learning workflow for Aligning mtDNA from NGS data

MitoScape v1.0

:: DESCRIPTION

MitoScape is a novel, big-data, software for extracting mitochondrial DNA sequences from NGS.

::DEVELOPER

Larry N. Singh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MitoScape

:: MORE INFORMATION

Citation

Singh LN, Ennis B, Loneragan B, Tsao NL, Lopez Sanchez MIG, Li J, Acheampong P, Tran O, Trounce IA, Zhu Y, Potluri P; Regeneron Genetics Center, Emanuel BS, Rader DJ, Arany Z, Damrauer SM, Resnick AC, Anderson SA, Wallace DC.
MitoScape: A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data.
PLoS Comput Biol. 2021 Nov 11;17(11):e1009594. doi: 10.1371/journal.pcbi.1009594. Epub ahead of print. PMID: 34762648.

RVS 20140305 – Genetic Association with NGS data

RVS 20140305

:: DESCRIPTION

The RVS (robust variance score) is a novel likelihood-based method for genetic association with NGS data from external control groups. RVS substitutes genotype calls by their expected values given observed sequence data and implements a robust variance estimate for the score statistic.

::DEVELOPER

Strug lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 RVS

:: MORE INFORMATION

Citation

Association analysis using next-generation sequence data from publicly available control groups: the robust variance score statistic.
Derkach A, Chiang T, Gong J, Addis L, Dobbins S, Tomlinson I, Houlston R, Pal DK, Strug LJ.
Bioinformatics. 2014 Apr 14. pii: btu196.

NgsAdmix 20130625 / FastNGSadmixPCA – Infer Ancestry Proportions from low depth NGS data

NgsAdmix 20130625 / FastNGSadmixPCA

:: DESCRIPTION

NGSadmix is a very nice tool for finding admixture proportions from NGS data. It is based on genotype likelihoods.

FastNGSadmixPCA  is a very fast tool for finding admixture proportions from NGS data of a single individual to incorporate into OCA of NGS data. It is based on genotype likelihoods.

::DEVELOPER

NgsAdmix team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler / R

:: DOWNLOAD

 NgsAdmix, FastNGSadmixPCA

:: MORE INFORMATION

Citation

Genetics. 2013 Nov;195(3):693-702. doi: 10.1534/genetics.113.154138. Epub 2013 Sep 11.
Estimating individual admixture proportions from next generation sequencing data.
Skotte L1, Korneliussen TS, Albrechtsen A.

REDItools 1.2.1 / REDItools2 – RNA editing detection by NGS data

REDItools 1.2.1 / REDItools2

:: DESCRIPTION

REDItools are python scripts developed with the aim to study RNA editing at genomic scale by next generation sequencing data.

REDItools2 is the optimized, parallel multi-node version of REDItools.

::DEVELOPER

Ernesto Picardi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 REDItools , REDItools2

:: MORE INFORMATION

Citation

Curr Protoc Bioinformatics. 2015 Mar 9;49:12.12.1-12.12.15. doi: 10.1002/0471250953.bi1212s49.
Using REDItools to Detect RNA Editing Events in NGS Datasets.
Picardi E1, D’Erchia AM, Montalvo A, Pesole G.

NgsRelate v2.0 – Estimating Pairwise Relatedness from NGS data

NgsRelate v2.0

:: DESCRIPTION

NgsRelate can be used to infer relatedness coefficients for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes.

::DEVELOPER

NgsRelate team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 NgsRelate

:: MORE INFORMATION

Citation

NgsRelate: a software tool for inferring pairwise relatedness from Next Generation Sequencing data.
Korneliussen TS, Moltke I.
Bioinformatics. 2015 Aug 30. pii: btv509

VirusHunter 0.7 – Analysis of NGS data for Detection of both Novel and Known Virus Sequences

VirusHunter 0.7

:: DESCRIPTION

VirusHunter is a fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.

::DEVELOPER

The Zhao Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 VirusHunter

:: MORE INFORMATION

Citation:

PLoS One. 2013 Oct 22;8(10):e78470. doi: 10.1371/journal.pone.0078470.
Identification of Novel Viruses Using VirusHunter — an Automated Data Analysis Pipeline.
Zhao G, Krishnamurthy S, Cai Z, Popov VL, Travassos da Rosa AP, Guzman H, Cao S, Virgin HW, Tesh RB, Wang D.

GENSENG 0.4 – Detecting CNVs from NGS data

GENSENG 0.4

:: DESCRIPTION

GENSENG is a software detecting CNVs(Copy Number Variations) from NGS(Next Generation Sequencing) data.

::DEVELOPER

Wei Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  GENSENG

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Feb 1;41(3):1519-32. doi: 10.1093/nar/gks1363. Epub 2012 Dec 28.
Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation.
Szatkiewicz JP1, Wang W, Sullivan PF, Wang W, Sun W.

AdapterRemoval v2.3.2 – NGS Data Trimming and Collapsing

AdapterRemoval v2.3.2

:: DESCRIPTION

AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3′ end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.

::DEVELOPER

The Centre for Anthropobiology and Genomics of Toulouse

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AdapterRemoval

:: MORE INFORMATION

Citation

Schubert M, Lindgreen S, Orlando L.
AdapterRemoval v2: rapid adapter trimming, identification, and read merging.
BMC Res Notes. 2016 Feb 12;9:88. doi: 10.1186/s13104-016-1900-2. PMID: 26868221; PMCID: PMC4751634.

Parallel-QC 1.0 – A Parallel Quality Control computational engine for NGS data

Parallel-QC 1.0

:: DESCRIPTION

Parallel-QC is a fast computational engine specifically designed for general NGS data QC. Parallel-QC can complete sequencing-quality assessment accuracy and efficiency. Possible contaminating species could also be identified without any prior information. And the whole processing of Parallel-QC is quite fast since it is optimized based on parallel computation.

::DEVELOPER

Bioinformatics Group , Single-cell Reseearch Center of Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences (QIBEBT-CAS).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 Parallel-QC

:: MORE INFORMATION

Citation

PLoS One. 2013;8(4):e60234. doi: 10.1371/journal.pone.0060234. Epub 2013 Apr 2.
QC-Chain: fast and holistic quality control method for next-generation sequencing data.
Zhou Q1, Su X, Wang A, Xu J, Ning K.

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