Tag: Parallel

ACME v1 – Efficient Parallel Motif Extraction from Very Long Sequences

ACME v1

:: DESCRIPTION

ACME (Advanced parallel motif extractor) is an advanced parallel motif extractor. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution.

::DEVELOPER

InfoCloud Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Compiler

:: DOWNLOAD

 ACME

:: MORE INFORMATION

Citation:

Majed Sahli, Essam Mansour, Panos Kalnis:
ACME: Efficient Parallel Motif Extraction from Very Long Sequences.
Technical Report

Ray 2.3.1 – Parallel Genome Assemblies for Parallel DNA sequencing

Ray 2.3.1

:: DESCRIPTION

Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data.

::DEVELOPER

Sébastien Boisvert

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Mac OsX/Windows
  • C++ Compiler

:: DOWNLOAD

 Ray

:: MORE INFORMATION

Citation

Genome Biol. 2012 Dec 22;13(12):R122. doi: 10.1186/gb-2012-13-12-r122.
Ray Meta: scalable de novo metagenome assembly and profiling.
Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J.

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.
Boisvert S, Laviolette F, Corbeil J.
Journal of Computational Biology November 2010, 17(11): 1519-1533.

PBOOST – Parallel Permutation Tests in Genome-wide Association Studies

PBOOST

:: DESCRIPTION

PBOOST is a GPU based tool for parallel permutation tests in genome-wide association studies.

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

PBOOST

:: REQUIREMENTS

:: DOWNLOAD

  PBOOST 

:: MORE INFORMATION

Citation:

PBOOST: a GPU-based tool for parallel permutation tests in genome-wide association studies.
Yang G, Jiang W, Yang Q, Yu W.
Bioinformatics. 2014 Dec 21. pii: btu840.

GRAPES 2.9 – SMP Querying system for Efficient Parallel Subgraph Isomorphism in databases of Graphs

GRAPES 2.9

:: DESCRIPTION

GRAPES is a querying system for parallel searching in databases of graphs, and single target graph, using symmetric multiprocessing (SMP) architectures. It implements a parallel version of well established graph searching algorithms providing efficient solutions for graphs indexing and matching.

::DEVELOPER

Alfredo Pulvirenti

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GRAPES

:: MORE INFORMATION

Citation:

GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures.
Giugno R, Bonnici V, Bombieri N, Pulvirenti A, Ferro A, Shasha D.
PLoS One. 2013 Oct 22;8(10):e76911. doi: 10.1371/journal.pone.0076911.

Parallel-QC 1.0 – A Parallel Quality Control computational engine for NGS data

Parallel-QC 1.0

:: DESCRIPTION

Parallel-QC is a fast computational engine specifically designed for general NGS data QC. Parallel-QC can complete sequencing-quality assessment accuracy and efficiency. Possible contaminating species could also be identified without any prior information. And the whole processing of Parallel-QC is quite fast since it is optimized based on parallel computation.

::DEVELOPER

Bioinformatics Group , Single-cell Reseearch Center of Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences (QIBEBT-CAS).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 Parallel-QC

:: MORE INFORMATION

Citation

PLoS One. 2013;8(4):e60234. doi: 10.1371/journal.pone.0060234. Epub 2013 Apr 2.
QC-Chain: fast and holistic quality control method for next-generation sequencing data.
Zhou Q1, Su X, Wang A, Xu J, Ning K.

GHOST-MP 1.3.4 – Parallel Sequence Similarity Search Tool

GHOST-MP 1.3.4

:: DESCRIPTION

GHOST-MP is a parallel sequence similarity search tool. It searches for similar sequences among nucleotide query sequences and amino acid sequence database like BLASTX.

::DEVELOPER

Akiyama Laboratory , Tokyo Institute of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

GHOST-MP

:: MORE INFORMATION

Citation

Int J Mol Sci. 2017 Oct 11;18(10). pii: E2124. doi: 10.3390/ijms18102124.
A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data.
Kakuta M, Suzuki S, Izawa K, Ishida T, Akiyama Y

RAxML 8.2.12 / RAxML-NG 0.9.0- Sequential and Parallel Maximum Likelihood based inference of large phylogenetic trees

RAxML 8.2.12 / RAxML-NG 0.9.0

:: DESCRIPTION

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.

RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. RAxML-NG is a successor of RAxML (Stamatakis 2014) and leverages the highly optimized likelihood computation implemented in libpll (Flouri et al. 2014).

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  RAxML , RAxML-NG

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Nov 1;35(21):4453-4455. doi: 10.1093/bioinformatics/btz305.
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.
Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A

Bioinformatics. 2014 May 1;30(9):1312-3. doi: 10.1093/bioinformatics/btu033. Epub 2014 Jan 21.
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Stamatakis A.

S.A. Berger, D. Krompaß, A. Stamatakis:
“Performance, Accuracy and Web-Server for Evolutionary Placement of Short Sequence Reads under maximum-likelihood“.
Systematic Biology 60(3):291-302, 2011.

ParDRe 2.2.5 – Faster Parallel Duplicated Reads Removal Tool for Sequencing Studies

ParDRe 2.2.5

:: DESCRIPTION

ParDRe is a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of Single-End or Paired-End sequences from fasta or fastq files.

::DEVELOPER

Jorge González Domínguez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ParDRe

:: MORE INFORMATION

Citation:

ParDRe: Faster Parallel Duplicated Reads Removal Tool for Sequencing Studies.
González-Domínguez J, Schmidt B.
Bioinformatics. 2016 Jan 22. pii: btw038.

Musket 1.1 – Parallel and Scalable Multistage K-mer Spectrum based Error Corrector for Illumina Sequence data

Musket 1.1

:: DESCRIPTION

Musket is an efficient multistage k-mer based corrector for Illumina short read data. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage workflow. Our performance evaluation results, in terms of correction quality and de novo genome assembly measures, reveal that Musket is consistently one of the top performing substitution-error-based correctors. In addition, Musket is multi-threaded using a master-slave model and demonstrates superior parallel scalability compared to all other evaluated correctors as well as a highly competitive overall execution time.

::DEVELOPER

Yongchao Liu, Dr.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 Musket

:: MORE INFORMATION

Citation

Yongchao Liu, Jan Schroeder and Bertil Schmidt:
“ Musket: a multistage k-mer spectrum based error corrector for Illumina sequence data“.
Bioinformatics, 2013, 29(3): 308-315