HISAT / HISAT2 2.0.3-beta – Hierarchical Indexing for Spliced Alignment of Transcripts

HISAT / HISAT2 2.0.3-beta

:: DESCRIPTION

HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads.

HISAT2 is a successor to both HISAT and TopHat2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 HISAT2

:: MORE INFORMATION

Citation

HISAT: a fast spliced aligner with low memory requirements.
Kim D, Langmead B, Salzberg SL.
Nat Methods. 2015 Apr;12(4):357-60. doi: 10.1038/nmeth.3317.

PALMapper 0.5 – Spliced Alignments of RNA-Seq Reads

PALMapper 0.5

:: DESCRIPTION

PALMapper, a fast and easy-to-use tool that is designed to accurately compute both unspliced and spliced alignments for millions of RNA-Seq reads. It combines the efficient read mapper GenomeMapper with the spliced aligner QPALMA, which exploits read-quality information and predictions of splice sites to improve the alignment accuracy.

::DEVELOPER

Rätsch Lab @ the Friedrich Miescher Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 PALMapper

:: MORE INFORMATION

Citation:

Jean, G., Kahles, A., Sreedharan, V.T., De Bona, F., Raetsch, G.,
RNA-Seq Read Alignments with PALMapper,
Curr. Protoc. Bioinform., 32:11.6.1-11.6.38, 2010.

ABMapper 2.0.4 – A suffix-array based Spliced Alignment tool

ABMapper 2.0.4

:: DESCRIPTION

ABMapper is a portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping.

::DEVELOPER

Hong Kong Bioinformatics Center & Department of Computer Science and Engineering, The Chinese University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Perl

:: DOWNLOAD

  ABMapper

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Feb 1;27(3):421-2. doi: 10.1093/bioinformatics/btq656. Epub 2010 Dec 17.
ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.
Lou SK, Ni B, Lo LY, Tsui SK, Chan TF, Leung KS.