Tag: Short Read

DecGPU 1.0.7 – Distributed short read Error Correction on GPUs

DecGPU 1.0.7

:: DESCRIPTION

DecGPUis the first parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models. Performan evaluation using simulated and real datasets revealed that our algorithm demonstrates superior performance, in terms of error correction quality and execution speed, to the Hybrid SHREC error correction algorithm The distributed feature of our algorithm makes it feasible and flexible for the error correction of large-scale datasets.

::DEVELOPER

Liu, Yongchao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CUDA toolkits and SDK 2.0 or higher.

:: DOWNLOAD

  DecGPU

:: MORE INFORMATION

Citation:

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell:
“DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI“.
BMC Bioinformatics, 2011, 12:85.

 

PASHA 1.0.10 – Parallelized Short Read Assembly

PASHA 1.0.10

:: DESCRIPTION

PASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, PASHA has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to produce better assemblies with comparable genome coverage and mis-assembly rates compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. Moreover, PASHA achieves the fastest speed for all three datasets on a single CPU.

::DEVELOPER

Liu, Yongchao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PASHA

:: MORE INFORMATION

Citation:

Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell:
” Parallelized short read assembly of large genomes using de Bruijn graphs“.
BMC Bioinformatics, 2011, 12:354

FermiKit 0.13 / fermi-lite 0.1- De novo Assembly based Variant Calling pipeline for Illumina Short Reads

FermiKit 0.13 / fermi-lite 0.1

:: DESCRIPTION

FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.

fermi-lite is a standalone C library as well as a command-line tool for assembling Illumina short reads in regions from 100bp to 10 million bp in size. Fermi-lite is largely a miniature of FermiKit.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FermiKit , fermi-lite

:: MORE INFORMATION

Citation

FermiKit: assembly-based variant calling for Illumina resequencing data.
Li H.
Bioinformatics. 2015 Nov 15;31(22):3694-6. doi: 10.1093/bioinformatics/btv440.

BAM_ABS – Bayesian Assignment Method for Ambiguous Bisulfite Short Reads

BAM-ABS

:: DESCRIPTION

BAM_ABS is a tool which simulates a Bayesian model that computes the posterior probability of mapping a multiread to each candidate genomic location, taking advantage of uniquely aligned reads.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

BAM_ABS

:: MORE INFORMATION

Citation

Tran H, Wu X, Tithi S, Sun MA, Xie H, Zhang L.
A Bayesian Assignment Method for Ambiguous Bisulfite Short Reads.
PLoS One. 2016 Mar 24;11(3):e0151826. doi: 10.1371/journal.pone.0151826. PMID: 27011215; PMCID: PMC4806927.

FASTX-Toolkit 0.0.14 – Short-Reads FASTA/FASTQ files Preprocessing

FASTX-Toolkit 0.0.14

:: DESCRIPTION

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs.However,It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome – manipulating the sequences to produce better mapping results.The FASTX-Toolkit tools perform some of these preprocessing tasks.

:: DEVELOPER

The Hannon laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  FASTX-Toolkit

:: MORE INFORMATION

TopHat 2.1.1 – Short Read Aligner for RNA-Seq Experiments

TopHat 2.1.1

:: DESCRIPTION

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

TopHat

:: MORE INFORMATION

Citation

Trapnell C, Pachter L, Salzberg SL.
TopHat: discovering splice junctions with RNA-Seq.
Bioinformatics (2009) 25(9): 1105-1111.

Genome Biology 2013, 14:R36
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley and Steven L Salzberg

Blue 1.1.3 – Short-read Error-correction tool

Blue 1.1.3

:: DESCRIPTION

Blue is a fast, accurate short-read error-correction tool based on k-mer consensus and context. It will correct both Illumina and 454-like data, and accepts sequence data files in both FASTQ and FASTA formats.

::DEVELOPER

CSIRO Transformational Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

Blue

:: MORE INFORMATION

Citation

Blue: correcting sequencing errors using consensus and context.
Greenfield P, Duesing K, Papanicolaou A, Bauer DC.
Bioinformatics. 2014 Jun 11. pii: btu368.

AREM 1.0.1 – Aligning Short Reads from ChIP-sequencing by Expectation Maximization

AREM 1.0.1

:: DESCRIPTION

AREM (Aligning reads by Expectation-Maximization) is a peak caller for ChIP-Seq experiments that robustly handles short reads with *multiple* possible mappings.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

  AREM

:: MORE INFORMATION

Citation:

J Comput Biol. 2011 Nov;18(11):1495-505. Epub 2011 Oct 28.
AREM: aligning short reads from ChIP-sequencing by expectation maximization.
Newkirk D, Biesinger J, Chon A, Yokomori K, Xie X.

Illuminator 20110419 – Mutation Detection using Short-read Clonal Sequencing

Illuminator 20110419

:: DESCRIPTION

Illuminator is a new sequence alignment program for the output from Illumina GA-II clonal sequencers. It is aimed primarily at kilobase-sized reference regions, as would typically be used in the context of mutation detection.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

Illuminator

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 Illuminator

:: MORE INFORMATION

Citation

Carr IM, Morgan JE, Diggle CP, Sheridan EG, Markham AF, Logan CV, Inglehearn CF, Taylor GR, Bonthron DT.
Illuminator, a desktop program for mutation detection using short-read clonal sequencing.
Genomics 2011 Oct;98(4):302-9.

ShotGun 1.0.10 – Flexible Short Read Simulator

ShotGun 1.0.10

:: DESCRIPTION

ShotGun is a flexible short read simulator. ShotGun generates sequence data with user-specified read length and average depth, accommodates to cycle specific sequencing error rates, allows the read depth distribution to be either the ideal Poisson or Negative Binomial to model the overdispersion observed with real sequencing data. In addition, ShotGun performs computationally efficient Single Nucleotide Polymorphism (SNP) discovery using a statistic aggregated across all sequenced samples. False positives can be controlled at any desired rate according to the null distribution of this multi-sample statistic.

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 ShotGun

:: MORE INFORMATION