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

:: 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.

FAVR 1.0 – Filtering and Annotation of Variants that are Rare

FAVR 1.0

:: DESCRIPTION

FAVR is a suite of new methods designed to work with commonly used MPS analysis pipelines to assist in the resolution of some of the issues related to the analysis of the vast amount of resulting data, with a focus on relatively rare genetic variants.

::DEVELOPER

Bernie Pope

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • PySam

:: DOWNLOAD

 FAVR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Feb 25;14:65. doi: 10.1186/1471-2105-14-65.
FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets.
Pope BJ1, Nguyen-Dumont T, Odefrey F, Hammet F, Bell R, Tao K, Tavtigian SV, Goldgar DE, Lonie A, Southey MC, Park DJ.

Portcullis 1.2.2 – Splice Junction Analysis and Filtering from BAM files

Portcullis 1.2.2

:: DESCRIPTION

Portcullis stands for PORTable CULLing of Invalid Splice junctions from pre-aligned RNA-seq data. It is known that RNAseq mapping tools generate many invalid junction predictions, particularly in deep datasets with high coverage over splice sites.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Portcullis

:: MORE INFORMATION

Citation

Gigascience. 2018 Dec 1;7(12). doi: 10.1093/gigascience/giy131.
Efficient and accurate detection of splice junctions from RNA-seq with Portcullis.
Mapleson D, Venturini L, Kaithakottil G, Swarbreck D.

Kontaminant – Kmer-based Screening and Filtering tool for Next-gen Sequencing Reads

Kontaminant

:: DESCRIPTION

Kontaminant is a kmer-based screening and filtering tool for next-gen sequencing reads.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 Kontaminant

:: MORE INFORMATION

Citation

Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.
Daly, G.M., Leggett, R.M., Rowe, W., Stubbs, S., Wilkinson, M., Ramirez-Gonzalez, R.H., Caccamo, M., Bernal, W., Heeney, J.L.
PLoS One. 2015 Jun 22;10(6):e0129059. doi: 10.1371/journal.pone.0129059

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