Tag: Short Read Sequence

BarraCUDA 0.7.0 – Short Read Sequence Aligner using Graphics Processing Units

BarraCUDA 0.7.0

:: DESCRIPTION

BarraCUDA is a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence.

::DEVELOPER

the Metabolic Research Laboratories

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • NVIDIA CUDA

:: DOWNLOAD

 BarraCUDA

:: MORE INFORMATION

Citation

BMC Res Notes. 2012 Jan 13;5:27. doi: 10.1186/1756-0500-5-27.
BarraCUDA – a fast short read sequence aligner using graphics processing units.
Klus P, Lam S, Lyberg D, Cheung MS, Pullan G, McFarlane I, Yeo GSh, Lam BY.

SRST 2-0.2.0 – Short Read Sequence Typing for Bacterial Pathogens

SRST 2-0.2.0

:: DESCRIPTION

SRST is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.

::DEVELOPER

Bernie Pope

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Python
  • bowtie2
  • SAMtools

:: DOWNLOAD

 SRST

:: MORE INFORMATION

Citation

Genome Med. 2014 Nov 20;6(11):90. doi: 10.1186/s13073-014-0090-6. eCollection 2014.
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs.
Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ, Tomita T, Zobel J, Holt KE

BMC Genomics. 2012 Jul 24;13:338.
Short read sequence typing (SRST): multi-locus sequence types from short reads.
Inouye M, Conway TC, Zobel J, Holt KE.

R2R 0.950 – Analysis of Short Read Sequence data obtained by NextGen Sequencing Techniques

R2R 0.950

:: DESCRIPTION

R2R (From Reads to Results) is a simple to use package for very sensitive analysis of short read sequence data obtained by NextGen sequencing techniques. R2R was developed in conjunction with data obtained on the Illumina GA platforms.

::DEVELOPER

Ole Skovgaard (olesk@ruc.dk )

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 R2R

:: MORE INFORMATION

Citation

Genome Res. 2011 Aug;21(8):1388-93. doi: 10.1101/gr.117416.110.
Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing.
Skovgaard O, Bak M, L?bner-Olesen A, Tommerup N.