Tag: Aligner

Bismark 0.23.1 – Aligner and Methylation Caller for Bisulfite-Seq Applications

Bismark 0.23.1

:: DESCRIPTION

Bismark is a program to align bisulfite treated sequencing reads (BS-Seq) to a reference genome and perform methylation calls for every cytosine in the read in a single step. The output can be easily imported into a genome viewer such as SeqMonk, enabling researchers to analyse their data straight away.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Bismark

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 1;27(11):1571-2. Epub 2011 Apr 14.
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.
Krueger F, Andrews SR.

BELLA v1.0 – Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper

BELLA v1.0

:: DESCRIPTION

BELLA is a computationally efficient and highly accurate long-read to long-read aligner and overlapper.

::DEVELOPER

PASSION Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BELLA

:: MORE INFORMATION

Citation

BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper
Giulia Guidi, Marquita Ellis, Daniel Rokhsar, Katherine Yelick, Aydın Buluç
bioRxiv 464420; doi: https://doi.org/10.1101/464420

Parallel T-Coffee 1.914 – Parallel Multiple Sequence Aligner based on TCoffee

Parallel T-Coffee 1.914

:: DESCRIPTION

Parallel T-Coffee (PTC) is the first parallel implementation of the TCoffee multiple sequence alignment tool. It has been developed to overcome main limitations of the original method. It is based on the MPI and RMA mechanisms, and it can be run on distributed memory clusters. PTC supports a majority of options provided by TCoffee 3.79, including the 3D-Coffee mode. It can be used to align data sets consisting of hundreds of proteins in reasonable time limits.

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • Perl

:: DOWNLOAD

 Parallel T-Coffee

:: MORE INFORMATION

Citation

J. Zola, X. Yang, S. Rospondek, S. Aluru
Parallel T-Coffee: A Parallel Multiple Sequence Aligner
In Proc. of ISCA PDCS-2007, pp. 248-253, 2007.

Satsuma2 – Whole-genome Synteny Aligner

Satsuma2

:: DESCRIPTION

Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences.

Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and complex DNA sequences providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accomodate the billions of base pairs in vertebrate genomes).

::DEVELOPER

Grabherr Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

Satsuma2

:: MORE INFORMATION

Citation

Grabherr MG, Russell P, Meyer M, Mauceli E, Alfoldi J, Di Palma F, Lindblad-Toh K.
Genome-wide synteny through highly sensitive sequence alignment: Satsuma.
Bioinformatics. 2010 May 1;26(9):1145-51. Epub 2010 Mar 5

RFA 0.1 – Random Field Aligner

RFA 0.1

:: DESCRIPTION

RFA is a method for aligning barcoded reads generated by a read cloud protocol such as 10X or Moleculo. Reads of the same barcode are aligned jointly to the reference genome. As a result, many of the repeats in the genome can be mapped.

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

RFA

:: MORE INFORMATION

Citation

Bishara A, Liu Y, Weng Z, Kashef-Haghighi D, Newburger DE, West R, Sidow A, Batzoglou S.
Read clouds uncover variation in complex regions of the human genome.
Genome Res. 2015 Oct;25(10):1570-80. doi: 10.1101/gr.191189.115. Epub 2015 Aug 18. PMID: 26286554; PMCID: PMC4579342.

ALFALFA 0.8.1 – A Long Fragment Aligner

ALFALFA 0.8.1

:: DESCRIPTION

The long read mapper ALFALFA achieves high performance in accurately mapping long (>500bp) single-end and paired-end reads to gigabase-scale reference genomes, while remaining competitive for mapping shorter (>100bp) reads.

::DEVELOPER

ALFALFA team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 ALFALFA

:: MORE INFORMATION

Citation

A Long Fragment Aligner called ALFALFA.
Vyverman M, Baets B, Fack V, Dawyndt P.
BMC Bioinformatics. 2015 May 15;16(1):159.

Maligner – Fast Ordered Restriction Map Aligner

Maligner

:: DESCRIPTION

Maligner is a tool for aligning molecular or insilico restriction maps to a reference map.

::DEVELOPER

Lee Mendelowitz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Maligner

:: MORE INFORMATION

Citation:

Maligner: a fast ordered restriction map aligner.
Mendelowitz LM, Schwartz DC, Pop M.
Bioinformatics. 2015 Dec 3. pii: btv711.

Novoalign 4.03.03 – Aligner Capable of Gapped Alignment for Illumina Short Reads

Novoalign 4.03.03

:: DESCRIPTION

Novoalign is an aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties.

::DEVELOPER

Novocraft Technologies

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 Novoalign

:: MORE INFORMATION

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.

ASGAL v1.1.6 – Alternative Splicing Graph ALigner

ASGAL v1.1.6

:: DESCRIPTION

ASGAL is a tool for detecting the alternative splicing events expressed in a RNA-Seq sample with respect to a gene annotation.

::DEVELOPER

AlgoLab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ASGAL

:: MORE INFORMATION

Citation

Denti L, Rizzi R, Beretta S, Vedova GD, Previtali M, Bonizzoni P.
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events.
BMC Bioinformatics. 2018 Nov 20;19(1):444. doi: 10.1186/s12859-018-2436-3. PMID: 30458725; PMCID: PMC6247705.

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