cutadapt v3.4 – Remove Adapter Sequences from DNA Sequencing reads

cutadapt v3.4

:: DESCRIPTION

Cutadapt removes adapter sequences from DNA high-throughput sequencing data. This is usually necessary when the read length of the machine is longer than the molecule that is sequenced, such as in microRNA data.

::DEVELOPER

Marcel Martin @ the Science for Life Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 cutadapt

:: MORE INFORMATION

Citation

Marcel Martin
Cutadapt removes adapter sequences from high-throughput sequencing reads
EMBnet.journal volume 17 pages 10–12

EagleEye 1.66 – Remove Background MS/MS Spectra

EagleEye 1.66

:: DESCRIPTION

EagleEye removes background MS/MS spectra by comparing them with a non-annotated collection of spectra, obtained from combined LC-MS/MS runs of control in-gel digests as well as identified in on-going proteomis projects.

::DEVELOPER

SUNYAEV LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Junqueira, M., Spirin, V., Balbuena, T. S., Waridel, P., Surendranath, V., Kryukov, G., Adzhubei, I., Thomas, H., Sunyaev, S. and Shevchenko, A.
Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification.
J Proteome Res. 2008 Aug;7(8):3382-95. Epub 2008 Jun 18.

De-Identifier – Remove Patient Identification from FCS file

De-Identifier

:: DESCRIPTION

DeID (De-Identifier) is used to remove patient identification from flow cytometry standard (FCS) data files.  This is achieved by writing a copy of the data file with selected keyword values removed.

::DEVELOPER

Francis L. Battye

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX /  Linux
  • Java

:: DOWNLOAD

 DeID

:: MORE INFORMATION

TagCleaner 0.16 – Detect and Remove Tag Sequences from Metagenomic datasets

TagCleaner 0.16

:: DESCRIPTION

TagCleaner is a tool to automatically detect and efficiently remove tag sequences (e.g. WTA or MID tags) from metagenomic datasets.

TagCleaner Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 TagCleaner 

:: MORE INFORMATION

Citation:

Schmieder R, Lim YW, Rohwer F, Edwards R
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets.
BMC Bioinformatics 2010, 11:341.

DeconSeq 0.4.3 – Detect and Remove Contaminations from Metagenomic datasets

DeconSeq 0.4.3

:: DESCRIPTION

DeconSeq is a tool to automatically detect and efficiently remove any type of known sequence contamination from metagenomic datasets. The tool uses a modified version of the BWA-SW aligner and can be applied to longer-read datasets (150+bp read length).

DeconSeq Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 DeconSeq

:: MORE INFORMATION

Citation:

Schmieder R and Edwards R
Fast identification and removal of sequence contamination from genomic and metagenomic datasets.
PLoS ONE 2011, 6:e17288

SVN – Remove Systematic Variation in Microarray Gene Expression data

SVN

:: DESCRIPTION

SVN (Systematic variation normalization) is a procedure for removing systematic variation in microarray gene expression data. Based on an analysis of how systematic variation contributes to variability in microarray data sets, the SVN procedure includes background subtraction determined from the distribution of pixel intensity values and log conversion, linear or non-linear regression, restoration or transformation, and multiarray normalization.

::DEVELOPER

Pierre R. Bushel, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

 SVN

:: MORE INFORMATION

Citation:

Chou JW, Paules RS, Bushel PR.
Systematic variation normalization in microarray data to get gene expression comparison unbiased.
J Bioinform Comput Biol. 2005 Apr;3(2):225-41.