riboPicker 0.4.3 – Identification and Removal of rRNA-like Sequences.

riboPicker 0.4.3

:: DESCRIPTION

riboPicker is a tool to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic datasets. The tool was designed to process longer-read datasets (150+bp read length), but works on 100+bp reads too.

riboPicker Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 riboPicker

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Feb 1;28(3):433-5. Epub 2011 Dec 6.
Identification and removal of ribosomal RNA sequences from metatranscriptomes.
Schmieder R, Lim YW, Edwards R.

ParDRe 2.2.5 – Faster Parallel Duplicated Reads Removal Tool for Sequencing Studies

ParDRe 2.2.5

:: DESCRIPTION

ParDRe is a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of Single-End or Paired-End sequences from fasta or fastq files.

::DEVELOPER

Jorge González Domínguez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ParDRe

:: MORE INFORMATION

Citation:

ParDRe: Faster Parallel Duplicated Reads Removal Tool for Sequencing Studies.
González-Domínguez J, Schmidt B.
Bioinformatics. 2016 Jan 22. pii: btw038.

CS-SCORE – Rapid Identification and Removal of human Genome Contaminants from Metagenomic datasets

CS-SCORE

:: DESCRIPTION

CS-SCORE is a novel algorithm that can rapidly identify (with high sensitivity) host sequences contaminating metagenomic datasets.

::DEVELOPER

CS-SCORE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CS-SCORE

:: MORE INFORMATION

Citation:

CS-SCORE: Rapid identification and removal of human genome contaminants from metagenomic datasets.
Haque MM, Bose T, Dutta A, Reddy CV, Mande SS.
Genomics. 2015 May 2. pii: S0888-7543(15)00075-0. doi: 10.1016/j.ygeno.2015.04.005.

FPB 1.1 – FingerPrint Background removal

FPB 1.1

:: DESCRIPTION

FPB is a new data-independent tool suitable for large scale projects as well as mapping of few clones.

::DEVELOPER

Istituto di Genomica Applicata and at University of Udine.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl
  • TCL/TK

:: DOWNLOAD

 FPB

:: MORE INFORMATION

Citation

Automated FingerPrint Background removal: FPB.
Scalabrin S, Morgante M, Policriti A.
BMC Bioinformatics. 2009 Apr 30;10:127.

FastUniq 1.1 – de novo Duplicates Removal tool for paired short DNA Sequences

FastUniq 1.1

:: DESCRIPTION

FastUniq is a fast de novo tool for removal of duplicates in paired short reads. FastUniq identifies duplicates by comparing sequences between read pairs and does not require complete genome sequences as prerequisites.

::DEVELOPER

FastUniq team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FastUniq

:: MORE INFORMATION

Citation

PLoS One. 2012;7(12):e52249. doi: 10.1371/journal.pone.0052249. Epub 2012 Dec 20.
FastUniq: a fast de novo duplicates removal tool for paired short reads.
Xu H1, Luo X, Qian J, Pang X, Song J, Qian G, Chen J, Chen S.