Tag: Barcode

sabre – A Barcode Demultiplexing and Trimming tool for FastQ files

sabre

:: DESCRIPTION

Sabre is a tool that will demultiplex barcoded reads into separate files. It will work on both single-end and paired-end data in fastq format. It simply compares the provided barcodes with each read and separates the read into its appropriate barcode file, after stripping the barcode from the read (and also stripping the quality values of the barcode bases). If a read does not have a recognized barcode, then it is put into the unknown file.

::DEVELOPER

UC Davis Bioinformatics Core

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Sabre

:: MORE INFORMATION

Bareback 1.0 – Barcode Back-Processing for low complexity Illumina libraries

Bareback 1.0

:: DESCRIPTION

Bareback is a tool to shuffle Illumina image files with low complexity sequence at the start of all sequences to the end.Bareback-processing allows the user to ‘move’ the raw images acquired by the Illumina Genome Analyser IIx from initial cycles with a very biased sequence composition to the end of the run. For samples with very biased initial sequences (such as restriction enzyme sites) and/or very high cluster densities this procedure can allow to a dramatic increase in sequence yield. This approach also works very well for custom-made multiplexing applications.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows /Mac OsX
  • Perl

:: DOWNLOAD

 Bareback

:: MORE INFORMATION

Citation

PLoS One. 2011 Jan 28;6(1):e16607.
Large scale loss of data in low-diversity illumina sequencing libraries can be recovered by deferred cluster calling.
Krueger F, Andrews SR, Osborne CS.

BARCODE – A fast Lossless Read Compression tool based on Bloom Filters

BARCODE

:: DESCRIPTION

BARCODE achieves highly efficient compression by using a reference genome, but completely circumvents the need for alignment, affording a great reduction in the time needed to compress.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • Python

:: DOWNLOAD

  BARCODE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014;15 Suppl 9:S7. doi: 10.1186/1471-2105-15-S9-S7. Epub 2014 Sep 10.
Fast lossless compression via cascading Bloom filters.
Rozov R, Shamir R, Halperin E.