MARRVEL v2 – Model organism Aggregated Resources for Rare Variant ExpLoration

MARRVEL v2

:: DESCRIPTION

MARRVEL aims to facilitate the use of public genetic resources to prioritize rare human gene variants for study in model organisms. To automate the search process and gather all the data in a simple display we extract data from human data bases (OMIM, ExAC, Geno2MP, DGV, and DECIPHER) for efficient variant prioritization. The protein sequences for six organisms (S. cerevisiae, C. elegans, D. melanogaster, D. rerio, M. musculus, and H. sapiens) are aligned with highlighted protein domain information via collaboration with DIOPT.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Wang J, Al-Ouran R, Hu Y, Kim SY, Wan YW, Wangler MF, Yamamoto S, Chao HT, Comjean A, Mohr SE; UDN, Perrimon N, Liu Z, Bellen HJ.
MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.
Am J Hum Genet. 2017 Jun 1;100(6):843-853. doi: 10.1016/j.ajhg.2017.04.010. Epub 2017 May 11. PMID: 28502612; PMCID: PMC5670038.

TITINdb – Database of Titin Structure, Sequence, Isoform, Variant and Disease Information

TITINdb

:: DESCRIPTION

TITINdb is a web application which integrates titin structure, sequence, isoform, variant and disease information.

::DEVELOPER

Fraternali lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Laddach A, Gautel M, Fraternali F.
TITINdb-a computational tool to assess titin’s role as a disease gene.
Bioinformatics. 2017 Nov 1;33(21):3482-3485. doi: 10.1093/bioinformatics/btx424. PMID: 29077808; PMCID: PMC5860166.

FamAnn 1.0 – Automated Variant Annotation pipeline to facilitate Target Discovery for Family-based Sequencing Studies

FamAnn 1.0

:: DESCRIPTION

FamAnn is an automated variant annotation pipeline designed for facilitating target discovery for family-based sequencing studies.

::DEVELOPER

McCombie lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux /Windows/ MacOsX
Perl

:: DOWNLOAD

FamAnn

:: MORE INFORMATION

Citation

FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies.
Yao J, Zhang KX, Kramer M, Pellegrini M, McCombie WR.
Bioinformatics. 2014 Jan 13.

FermiKit 0.13 / fermi-lite 0.1- De novo Assembly based Variant Calling pipeline for Illumina Short Reads

FermiKit 0.13 / fermi-lite 0.1

:: DESCRIPTION

FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.

fermi-lite is a standalone C library as well as a command-line tool for assembling Illumina short reads in regions from 100bp to 10 million bp in size. Fermi-lite is largely a miniature of FermiKit.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

FermiKit , fermi-lite

:: MORE INFORMATION

Citation

FermiKit: assembly-based variant calling for Illumina resequencing data.
Li H.
Bioinformatics. 2015 Nov 15;31(22):3694-6. doi: 10.1093/bioinformatics/btv440.

Isaac / isaac_aligner 01.15.04.01 / isaac_variant_caller 1.0.7 – Genome Aligner and Variant Caller

Isaac / isaac_aligner 01.15.04.01 / isaac_variant_caller 1.0.7

:: DESCRIPTION

Isaac is ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. An ultrafast DNA sequence aligner /isaac_aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (isaac_variant_caller– Isaac Variant Caller) have been developed.

::DEVELOPER

Illumina, Inc.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

Isaac

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 15;29(16):2041-3. doi: 10.1093/bioinformatics/btt314. Epub 2013 Jun 4.
Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms.
Raczy C, Petrovski R, Saunders CT, Chorny I, Kruglyak S, Margulies EH, Chuang HY, Källberg M, Kumar SA, Liao A, Little KM, Strömberg MP, Tanner SW.

VarScan 2.4.0 – Variant Caller for Short Sequence Reads

VarScan 2.4.0

:: DESCRIPTION

VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequencyh. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples.

::DEVELOPER

The McDonnell Genome Institute (MGI) at Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / Mac OsX
Java

:: DOWNLOAD

VarScan

:: MORE INFORMATION

Citation:

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, & Ding L (2009).
VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
Bioinformatics (Oxford, England), 25 (17), 2283-5 PMID:

VIPER v1.0.3 – Variant InsPector and Expert Rating tool

VIPER v1.0.3

:: DESCRIPTION

VIPER can be utilised to view variant calls and decide whether or not those are true or false positives. All calls are visualised using IGV, thus enabling fast rating of sv calls.

::DEVELOPER

VIPER team

:: SCREENSHOTS

N/A.

:: REQUIREMENTS

Linux

:: DOWNLOAD

VIPER

:: MORE INFORMATION

Citation

Wöste M, Dugas M.
VIPER: a web application for rapid expert review of variant calls.
Bioinformatics. 2018 Jun 1;34(11):1928-1929. doi: 10.1093/bioinformatics/bty022. PMID: 29346510; PMCID: PMC5972565.

Variant Tool Chest 0.9.3 alpha – Analyzing Variants

Variant Tool Chest 0.9.3 alpha

:: DESCRIPTION

The Variant Tool Chest (VTC) is designed to be a tool chest for analyzing variants (particularly VCF files)

::DEVELOPER

VTC team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

MacOsX / Linux
Java

:: DOWNLOAD

Variant Tool Chest

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014;15 Suppl 7:S12. doi: 10.1186/1471-2105-15-S7-S12. Epub 2014 May 28.
Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files.
Ebbert MT, Wadsworth ME, Boehme KL, Hoyt KL, Sharp AR, O’Fallon BD, Kauwe JS, Ridge PG.

ClinSeK 1.2e – Targeted Variant Characterization Framework for Clinical Sequencing

ClinSeK 1.2e

:: DESCRIPTION

ClinSeK is a targeted sequence analysis toolkit that allows quick and sensitive investigation of genetic variation at sites of interest from high-throughput sequencing data.

::DEVELOPER

Zhou lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ClinSeK

:: MORE INFORMATION

Citation

ClinSeK: a targeted variant characterization framework for clinical sequencing.
Zhou W, Zhao H, Chong Z, Mark RJ, Eterovic AK, Meric-Bernstam F, Chen K.
Genome Med. 2015 Mar 31;7(1):34. doi: 10.1186/s13073-015-0155-1.

OVA – Ontology Variant Analysis Tool

OVA

:: DESCRIPTION

OVA (ontology variant analysis) is an online variant filtering and prioritisation application. Ontology Variant Analysis Tool can filter your VCF files on a wide array of criteria. Remaining genes are prioritisated based on their functional and phenotypic profile similarity to a user supplied phenotype.

::DEVELOPER

OVA Team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization.
Antanaviciute A, Watson CM, Harrison SM, Lascelles C, Crinnion L, Markham AF, Bonthron DT, Carr IM.
Bioinformatics. 2015 Aug 12. pii: btv473.