Tag: DNA Sequence Read

SnoWhite 2.0.3 – An Aggressive Cleaning Pipeline for DNA Sequence Reads

SnoWhite 2.0.3

:: DESCRIPTION

Snowhite is a pipeline designed to flexibly and aggressively clean sequence reads (gDNA or cDNA) prior to assembly. It takes in and returns fasta formatted sequence and (optionally) quality files.

::DEVELOPER

The Dlugosch Lab @ The University of Arizona

:: SCREENSHOTS

N/A

::  REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 SnoWhite

:: MORE INFORMATION

Citation

EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics.
Barker MS, Dlugosch KM, Dinh L, Challa RS, Kane NC, King MG, Rieseberg LH.
Evol Bioinform Online. 2010 Oct 20;6:143-9. doi: 10.4137/EBO.S5861.

DSRC 2.0 RC2 – DNA Sequence Reads Compression

DSRC 2.0 RC2

:: DESCRIPTION

DSRC is an application designed for compression of data files containing reads from DNA sequencing in FASTQ format. The amount of such files can be huge, e.g., a few (or tens) of gigabytes, so a need for a robust data compression tool is clear. Usually universal compression programs like gzip or bzip2 are used for this purpose, but it is obvious that a specialized tool can work better.

::DEVELOPER

REFRESH Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX / Windows
  • C++ Compiler

:: DOWNLOAD

 DSRC

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 18. pii: btu208.
DSRC 2-Industry-oriented compression of FASTQ files.
Roguski L, Deorowicz S.

S. Deorowicz and Sz. Grabowski,
Compression of DNA sequence reads in FASTQ format,
Bioinformatics (2011) 27(6):860–862.