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

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