Tag: Aligner

MICA-aligner r345 – Next-generation sequencing short reads aligner based on Intel MIC

MICA-aligner r345

:: DESCRIPTION

MICA-aligner is a new short-read aligner that is optimized in view of MIC’s limitation and the extra parallelism inside each MIC core.

::DEVELOPER

MICA-aligner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MICA-aligner

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 Apr 23;16 Suppl 7:S10. doi: 10.1186/1471-2105-16-S7-S10. Epub 2015 Apr 23.
MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC).
Luo R, Cheung J, Wu E, Wang H, Chan SH, Law WC, He G, Yu C, Liu CM, Zhou D, Li Y, Li R, Wang J, Zhu X, Peng S, Lam TW.

MOSAIK 2.2.3 – Aligner for Next-generation Sequencing Technologies

MOSAIK 2.2.3

:: DESCRIPTION

MOSAIK is a reference-guided assembler comprising of below modular programs:

  • MosaikBuild
  • MosaikAligner

MosaikBuild converts various sequence formats into Mosaik’s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences and produces BAMs as outputs.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX

:: DOWNLOAD

 MOSAIK

:: MORE INFORMATION

Citation

PLoS One. 2014 Mar 5;9(3):e90581. doi: 10.1371/journal.pone.0090581. eCollection 2014.
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping.
Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT.

HISEA – HIerarchical SEed Aligner

HISEA

:: DESCRIPTION

HISEA is a new long read aligner customized for Pacific Biosciences Single Molecule, Real-Time (SMRT) sequencing.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

HISEA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2017 Dec 19;18(1):564. doi: 10.1186/s12859-017-1953-9.
HISEA: HIerarchical SEed Aligner for PacBio data.
Khiste N, Ilie L

MXSCARNA 2.1 – Multiplex Stem Candidate Aligner for RNAs

MXSCARNA 2.1

:: DESCRIPTION

MXSCARNA is a tool for fast structural multiple alignment of RNA sequences using progressive alignment based on pairwise structural alignment algorithm of SCARNA.

::DEVELOPER

Asai’s Lab. Computational Biology Research Center (CBRC),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MXSCARNA

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Jun 15;25(12):1498-505. doi: 10.1093/bioinformatics/btp261. Epub 2009 Apr 17.
A local multiple alignment method for detection of non-coding RNA sequences.
Tabei Y, Asai K.

KARMA 0.9 – Aligner for Mapping Shotgun Sequencer FASTQ Read

KARMA 0.9

:: DESCRIPTION

Karma ( K-tuple Alignment with Rapid Matching Algorithm) is an index based high speed aligner for mapping shotgun sequencer FASTQ reads to a reference genome. Karma assembles FASTQ files from Solexa into a set of mapped reads using a genome reference. It does this by first creating a index of the genome reference, then uses portions of the read to index into the reference to find possible matches.

::DEVELOPER

Paul Anderson @ the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 KARMA

:: MORE INFORMATION

Exit mobile version