Tag: Read-mapping

TreQ 0.1 beta – Indel-tolerant Read mapping

TreQ 0.1 beta

:: DESCRIPTION

TreQ is a read mapper for high-throughput DNA sequencing reads, in particular reads from 100 nt to hundreds of nucleotides, and for large edit distance between sequencing read and match in the reference genome.

::DEVELOPER

Schliep lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 TreQ

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):i325-i332. doi: 10.1093/bioinformatics/bts380.
Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees.
Mahmud MP, Wiedenhoeft J, Schliep A.

HPG Aligner 2.0.1 – NGS Read Mapping

HPG Aligner 2.0.1

:: DESCRIPTION

HPG Aligner is an ultrafast and highly sensitive Next-Generation Sequencing (NGS) read mapping.

::DEVELOPER

Open source for Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HPG Aligner

:: MORE INFORMATION

Citation

Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.
Tárraga J, Arnau V, Martínez H, Moreno R, Cazorla D, Salavert-Torres J, Blanquer-Espert I, Dopazo J, Medina I.
Bioinformatics. 2014 Aug 20. pii: btu553.

PerM 0.4.0 – Read-mapping software based on Periodic Spaced Seeds for both Illumina and SOLiD sequencing data

PerM 0.4.0

:: DESCRIPTION

PerM is a software package which was designed to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. Today PerM is capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 PerM

:: MORE INFORMATION

Citation:

Yangho Chen, Tade Souaiaia and Ting Chen
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
Bioinformatics (2009) 25 (19): 2514-2521.

SToRM 0.0099 – Seed-based Read Mapping tool for SOLiD or Illumina sequencing data

SToRM 0.0099

:: DESCRIPTION

SToRM is a software tool primarily proposed for mapping SOLiD reads or Illumina reads to a reference genome. It was based on seeding techniques adapted to the statistical characteristics of the reads: the default seeds are for example designed (using the Iedera software) to comply with the properties of the SOLiD color encoding, or Illumina more classical encoding as well as the observed reading error distribution along the read.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 SToRM

:: MORE INFORMATION

Citation

Noé, L. and Gîrdea,. and Kucherov, G.:
Designing efficient spaced seeds for SOLiD read mapping
Advances in Bioinformatics, Volume 2010 2010

BM-Map 2.0.1 – Refining Next-Generation Sequencing (NGS) Read Mapping

BM-Map 2.0.1

:: DESCRIPTION

BM-Map is a powerful NGS genomic loci mapping refiner. It improves the mapping of the multireads (reads mapped to more than one genomic location with similar fidelities), as a refinement step after the general read-alignment is completed.

::DEVELOPER

Yuan Ji Lab  and Dr. Han Liang’s group.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 BM-Map

:: MORE INFORMATION

Citation

BMC Genomics. 2012;13 Suppl 8:S9. doi: 10.1186/1471-2164-13-S8-S9. Epub 2012 Dec 17.
BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data.
Yuan Y1, Norris C, Xu Y, Tsui KW, Ji Y, Liang H.

Biometrics. 2011 Dec;67(4):1215-24. doi: 10.1111/j.1541-0420.2011.01605.x. Epub 2011 Apr 22.
BM-map: Bayesian mapping of multireads for next-generation sequencing data.
Ji Y, Xu Y, Zhang Q, Tsui KW, Yuan Y, Norris C Jr, Liang S, Liang H.

CNVnator 0.3 – CNV Discovery and Genotyping from Depth of Read Mapping

CNVnator 0.3

:: DESCRIPTION

CNVnator is a tool for Copy number variation (CNV) discovery and genotyping from depth of read mapping.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CNVnator

:: MORE INFORMATION

Citation:

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
Abyzov A, Urban AE, Snyder M, Gerstein M.
Genome Res. 2011 Jun;21(6):974-84. Epub 2011 Feb 7.