VARIFI – Variant Identification, Filtering and Annotation of Amplicon Sequencing Data

VARIFI

:: DESCRIPTION

VARIFI is a pipeline for finding reliable genetic variants (single nucleotide polymorphisms (SNPs) and insertions and deletions (indels)).

::DEVELOPER

the Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

VARIFI-Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data.
Krunic M, Venhuizen P, Müllauer L, Kaserer B, von Haeseler A.
J Pers Med. 2019 Feb 1;9(1). pii: E10. doi: 10.3390/jpm9010010.

TCS – Evaluation and Filtering of multiple Sequence Alignments

TCS

:: DESCRIPTION

TCS (Transitive Consistency Score) web server is a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.
Chang JM, Di Tommaso P, Lefort V, Gascuel O, Notredame C.
Nucleic Acids Res. 2015 Apr 8. pii: gkv310.

Reaper 16-098 – Demultiplexing, Trimming and Filtering Short Read Sequencing data

Reaper 16-098

:: DESCRIPTION

Reaper is a program for demultiplexing, trimming and filtering short read sequencing data. It is intended to be suitable for dealing with a wide range of sequencing protocols, and will be updated to support new protocols where the current set of features does not suffice

::DEVELOPER

Stijn van Dongen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • C Compiler

:: DOWNLOAD

 Reaper

:: MORE INFORMATION

VariantBam 1.2.1 – Filtering and Profiling of Next-generational Sequencing data using Region-specific Rules

VariantBam 1.2.1

:: DESCRIPTION

VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files.

::DEVELOPER

VariantBam team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 VariantBam

:: MORE INFORMATION

Citation:

VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules.
Wala J, Zhang CZ, Meyerson M, Beroukhim R.
Bioinformatics. 2016 Feb 26. pii: btw111.

gffread 0.94f – Filtering, Converting and Manipulating GFF files

gffread 0.94f

:: DESCRIPTION

The program gffread can be used to validate, filter, convert and perform various other operations on GFF (General Feature Format) files.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 gffread

:: MORE INFORMATION

fqtrim 0.95 – Trimming & Filtering of Next-gen Reads

fqtrim 0.95

:: DESCRIPTION

fqtrim is a software utility for filtering and trimming high-throughput next-gen reads.

::DEVELOPER

Center for Computational Biology , Johns Hopkins University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  fqtrim

:: MORE INFORMATION

Mendelian – Heuristic Variant Filtering

Mendelian

:: DESCRIPTION

Mendelian is an R package that can be used to filter sequencing variants. It enables filtering for both dominant and recessive traits, with a wide variety of options (including reduced penetrance and detectance).

::DEVELOPER

Mendelian team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 Mendelian

:: MORE INFORMATION

Citation

An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors.
Broeckx BJ, Coopman F, Verhoeven G, Bosmans T, Gielen I, Dingemanse W, Saunders JH, Deforce D, Van Nieuwerburgh F.
BMC Bioinformatics. 2015 Nov 19;16:391. doi: 10.1186/s12859-015-0822-7.

Customized siDesigner – Design siRNA with Functional Off-target Filtering

Customized siDesigner

:: DESCRIPTION

Csidesigner (Customized siDesigner) is an siRNA selection tool with functional off-target filtering

::DEVELOPER

Jayprokas Chakrabarti lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Customized siDesigner

:: MORE INFORMATION

Citation:

Das S, Ghosal S, Kozak K, Chakrabarti J. (2012)
An siRNA designing tool with a unique functional off-target filtering approach.
J Biomol Struct Dyn. DOI: 10.1080/07391102.2012.736758

TrioVis 20130409 – Visualization approach for Filtering Genomic Variants of Parent-child Trios

TrioVis 20130409

:: DESCRIPTION

TrioVis is a visualisation tool developed to assist filtering on coverage and variant frequency for genomic variants from exome sequencing of parent-child trios. It organises the variant data by grouping each variant based on the laws of Mendelian inheritance. Taking three Variant Call Format (VCF) files as input, the tool provides a user interface to test different coverage thresholds (i.e. different levels of stringency), to find the optimal threshold values, and to gain insights into the global effects of filtering.

::DEVELOPER

Bioinformatics Research Group, Belgium

:: SCREENSHOTS

TrioVis

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

TrioVis

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 15;29(14):1801-2. doi: 10.1093/bioinformatics/btt267. Epub 2013 May 8.
TrioVis: a visualization approach for filtering genomic variants of parent-child trios.
Sakai R, Sifrim A, Vande Moere A, Aerts J.

GermlineFilter 1.2 – Encrypted Filtering of Germline Calls from Somatic vcf

GermlineFilter 1.2

:: DESCRIPTION

Germline Filter is a Python program used in the ICGC-TCGA DREAM Mutation Calling Challenge meant to contribute to the real data security measures.

::DEVELOPER

Boutros Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 GermlineFilter

:: MORE INFORMATION