Trimmomatic 0.39 – A Flexible Read Trimming tool for Illumina NGS data

Trimmomatic 0.39

:: DESCRIPTION

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.

::DEVELOPER

Usadel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

  Trimmomatic

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 28.
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM1, Lohse M, Usadel B.

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

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

UrQt 1.0.17 – Unsupervised Quality Trimming for NGS data

UrQt 1.0.17

:: DESCRIPTION

UrQt is a new quality control method for Unsupervised Quality trimming of Next Generation Sequencing reads

:: DEVELOPER

The Biometry and Evolutionary Biology laboratory (LBBE)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 UrQt

:: MORE INFORMATION

Citation

UrQt: an efficient software for the Unsupervised Quality trimming of NGS data
Modolo L, Lerat E.
BMC Bioinformatics. 2015 Apr 29;16(1):137.

NxTrim 0.3.0a – Optimized Trimming of Illumina Mate Pair Reads

NxTrim 0.3.0a

:: DESCRIPTION

nxtrim: Software to remove Nextera Mate Pair adapters and categorise reads according to the orientation implied by the adapter location.

::DEVELOPER

Illumina

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • BOOST

:: DOWNLOAD

 NxTrim

:: MORE INFORMATION

Citation

NxTrim: optimized trimming of Illumina mate pair reads.
O’Connell J, Schulz-Trieglaff O, Carlson E, Hims MM, Gormley NA, Cox AJ.
Bioinformatics. 2015 Feb 5. pii: btv057

PRUNETREE 5.0 – Trimming Taxa Off Phylogenies

PRUNETREE 5.0

:: DESCRIPTION

Prunetree is a program for trimming taxa off phylogenies. You can make subtrees by either including (or excluding) a specific group of taxa. In addition, it also has options to arbitrarily transform internode branch lengths (BL) following a speciational model (all BL = 1) or following Pagel?s method (all taxa aligned and all internode BL = 1).

::DEVELOPER

The Lajeunesse Lab

:: SCREENSHOTS

PRUNETREE

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 PRUNETREE

 :: MORE INFORMATION

Figaro 1.05 – Novel Vector Trimming software

Figaro 1.05

:: DESCRIPTION

Figaro is a software tool for identifying and removing the vector from raw DNA sequence data without prior knowledge of the vector sequence. By statistically modeling short oligonucleotide frequencies within a set of reads, Figaro is able to determine which DNA words are most likely associated with vector sequence.

::DEVELOPER

Figaro Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Figaro

:: MORE INFORMATION

Citation:

James Robert White, Michael Roberts, James A. Yorke and Mihai Pop
Figaro: a novel statistical method for vector sequence removal
Bioinformatics (2008) 24 (4): 462-467.