Tag: Whole-genome Sequencing

ShatterSeek v0.5 – Identification of Chromothripsis Events from Whole-genome Sequencing data

ShatterSeek v0.5

:: DESCRIPTION

ShatterSeek is an R package that provides utilities to detect chromothripsis events from next-generation sequencing (NGS) data. It takes as input copy number (CN) and structural variation (SV) calls calculated with the user preferred method. Hence, it is compatible with virtually any CN and SV caller.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R

:: DOWNLOAD

ShatterSeek

:: MORE INFORMATION

Citation

Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS; PCAWG Structural Variation Working Group, Park PJ; PCAWG Consortium.
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing.
Nat Genet. 2020 Mar;52(3):331-341. doi: 10.1038/s41588-019-0576-7. Epub 2020 Feb 5. Erratum in: Nat Genet. 2020 May 13;: PMID: 32025003; PMCID: PMC7058534.

MosaicForecast – Identification of Somatic Mutation from bulk Whole-genome Sequencing data

MosaicForecast

:: DESCRIPTION

MosaicForecast is machine learning method that leverages read-based phasing and read-level features to accurately detect mosaic SNVs (SNPs, small indels) from NGS data. It builds on existing algorithms to achieve a multifold increase in specificity.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R
  • Python

:: DOWNLOAD

MosaicForecast

:: MORE INFORMATION

Citation

Dou Y, Kwon M, Rodin RE, Cortés-Ciriano I, Doan R, Luquette LJ, Galor A, Bohrson C, Walsh CA, Park PJ.
Accurate detection of mosaic variants in sequencing data without matched controls.
Nat Biotechnol. 2020 Mar;38(3):314-319. doi: 10.1038/s41587-019-0368-8. Epub 2020 Jan 6. PMID: 31907404; PMCID: PMC7065972.

BIC-seq 2 0.2.4 – Copy Number analysis from Whole-genome Sequencing data

BIC-seq 2 0.2.4

:: DESCRIPTION

BIC-seq can accurately and efficiently identify CNVs via minimizing the Bayesian information criterion.Using BIC-seq, we identified hundreds of CNVs as small as 40 bp in the cancer genome sequenced at 10× coverage, whereas we could only detect large CNVs (> 15 kb) in the array comparative genomic hybridization profiles for the same genome.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R package / Perl

:: DOWNLOAD

 BIC-seq

:: MORE INFORMATION

Citation

Xi et al,
Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion
PNAS, 2011 November 15, 2011 vol. 108 no. 46

Indexcov – Fast Coverage Quality Control for Whole-genome Sequencing

Indexcov

:: DESCRIPTION

Indexcov is an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GO

:: DOWNLOAD

Indexcov

:: MORE INFORMATION

Citation:

Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix090.
Indexcov: fast coverage quality control for whole-genome sequencing.
Pedersen BS1,2, Collins RL3,4,5, Talkowski ME3,6,4,5, Quinlan AR

MarViN 0.1.0 – Rapid Genotype Refinement for Whole-Genome Sequencing Data using Multi-Variate Normal Distribution

MarViN 0.1.0

:: DESCRIPTION

MarViN is an algorithm that models  linkage-disequilibrium (LD) using a simple multivariate Gaussian distribution.

::DEVELOPER

Illumina

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MarViN

:: MORE INFORMATION

Citation:

Rapid genotype refinement for whole-genome sequencing data using multi-variate normal distributions.
Arthur R, O’Connell J, Schulz-Trieglaff O, Cox AJ.
Bioinformatics. 2016 Mar 9. pii: btw097

RareVariantVis 2.20.0 – Visualization of Rare Variants in Whole Genome Sequencing data

RareVariantVis 2.20.0

:: DESCRIPTION

RareVariantVis is a new tool for analysis of genome sequence data (including non-coding regions) for both germ line and somatic variants.

::DEVELOPER

Tomasz Stokowy <tomasz.stokowy at k2.uib.no>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 RareVariantVis

:: MORE INFORMATION

Citation

RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data.
Stokowy T, Garbulowski M, Fiskerstrand T, Holdhus R, Labun K, Sztromwasser P, Gilissen C, Hoischen A, Houge G, Petersen K, Jonassen I, Steen VM.
Bioinformatics. 2016 Jun 10. pii: btw359.

gSearch – Search tool for Whole-genome Sequencing

gSearch

:: DESCRIPTION

gSearch is a fast and flexible general search tool for whole-genome sequencing

::DEVELOPER

Soongsil University Machine Learning Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MacOsX

:: DOWNLOAD

 gSearch

:: MORE INFORMATION

Citation

gSearch: a fast and flexible general search tool for whole-genome sequencing.
Song T, Hwang KB, Hsing M, Lee K, Bohn J, Kong SW.
Bioinformatics. 2012 Aug 15;28(16):2176-7. doi: 10.1093/bioinformatics/bts358

MegaMapper 1.01e – Software for Positional Cloning of Mutations by Whole Genome Sequencing

MegaMapper 1.01e

:: DESCRIPTION

MegaMapper is a computational pipeline for positional cloning of mutations by whole genome sequencing.

::DEVELOPER

the Megason Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MegaMapper

:: MORE INFORMATION

Citation

Development. 2012 Nov;139(22):4280-90. doi: 10.1242/dev.083931. Epub 2012 Oct 10.
Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing.
Obholzer N, Swinburne IA, Schwab E, Nechiporuk AV, Nicolson T, Megason SG.