Scythe 0.994 – A Bayesian Adapter Trimmer

Scythe 0.994

:: DESCRIPTION

Scythe is a contaminant/adapter removal tool. It uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3′-end adapters, which often include poor quality bases.

::DEVELOPER

UC Davis Bioinformatics Core

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Scythe

:: MORE INFORMATION

ngsShoRT 2.2 – A Next Generation Sequencing Short Read Trimmer

ngsShoRT 2.2

:: DESCRIPTION

ngsShoRT algorithms are designed to pre-process Single Read (SR) or Paired-end (PE)/Mate-pair (MP) reads in FastQ format or Illumina’s native QSEQ format (with compressed file support). It privides parallel processing by multi-threading to deal with large volume of data and reduce running time. Another unique feature of ngsShoRT is that it was designed to handle PE/MP reads generically using paired-end specific modules.

::DEVELOPER

ngsShoRT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ngsShoRT

:: MORE INFORMATION

Citation

Software for pre-processing Illumina next-generation sequencing short read sequences.
Chen C, Khaleel SS, Huang H, Wu CH.
Source Code Biol Med. 2014 May 3;9:8. doi: 10.1186/1751-0473-9-8

Skewer 0.2.2 – Adapter Trimmer for Next-generation Sequencing Paired-end Reads

Skewer 0.2.2

:: DESCRIPTION

Skewer implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences.

::DEVELOPER

Hongshan Jiang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Skewer

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jun 12;15:182. doi: 10.1186/1471-2105-15-182.
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
Jiang H, Lei R, Ding SW, Zhu S