Tablet 1.19.09.03 – Next Generation Sequence Assembly Visualization

Tablet 1.19.09.03

:: DESCRIPTION

Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine.

::DEVELOPER

Information & Computational Sciences, The James Hutton Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 Tablet

:: MORE INFORMATION

Citation

Milne, I, Bayer, M, Cardle, L, Shaw, P, Stephen, G, Wright, F and Marshall, D. 2010.
Tablet – next generation sequence assembly visualization.
Bioinformatics 26(3), 401-402.

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

TriMetAss 1.2 – The Trinity-based Iterative Metagenomics Assembler

TriMetAss 1.2

:: DESCRIPTION

TriMetAss is an extension to the Trinity software , which can assemble select regions surrounding interesting features in metagenomic data

::DEVELOPER

Johan Bengtsson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux  / MacOsX
  • Java
  • Trinity

:: DOWNLOAD

 TriMetAss

:: MORE INFORMATION

Citation:

Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ:
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India.
Frontiers in Microbiology, Volume 5, Issue 648 (2014). doi: 10.3389/fmicb.2014.00648

OMWare 1.0 – Efficient Assembly of Genome-wide Physical Maps

OMWare 1.0

:: DESCRIPTION

OMWare is a tool that efficiently generated 405 de novo map assemblies of a single datasets collected from the cotton species Gossypium raimondii.

::DEVELOPER

Aaron Sharp

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

 OMWare

:: MORE INFORMATION

Citation

OMWare: a tool for efficient assembly of genome-wide physical maps.
Sharp AR, Udall JA.
BMC Bioinformatics. 2016 Jul 25;17 Suppl 7:241. doi: 10.1186/s12859-016-1099-1.

LightAssembler – Lightweight Resources Assembly Algorithm

LightAssembler

:: DESCRIPTION

LightAssembler is a lightweight assembly algorithm designed to be executed on a desktop machine. It uses a pair of cache oblivious Bloom filters, one holding a uniform sample of g-spaced sequenced k-mers and the other holding k-mers classified as likely correct, using a simple statistical test.

::DEVELOPER

Sara El-Metwally

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LightAssembler

:: MORE INFORMATION

Citation

LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads.
El-Metwally S, Zakaria M, Hamza T.
Bioinformatics. 2016 Jul 13. pii: btw470.

QUAST 4.1 – Quality Assessment Tool for Genome Assemblies

QUAST 4.1

:: DESCRIPTION

QUAST evaluates a quality of genome assemblies by computing various metrics and providing nice reports.

MetaQUAST evaluates and compares metagenome assemblies based on alignments to close references.

Icarus is a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on QUAST genome quality assessment tool

::DEVELOPER

Algorithmic Biology Lab at St. Petersburg Academic University of the Russian Academy of Sciences

:: SCREENSHOTS

MetaQUAST

:: REQUIREMENTS

  • Linux /  MacOsX
  • Python
  • Perl
  • MUMmer

:: DOWNLOAD

 QUAST

:: MORE INFORMATION

Citation

Icarus: visualizer for de novo assembly evaluation.
Mikheenko A, Valin G, Prjibelski A, Saveliev V, Gurevich A.
Bioinformatics. 2016 Jul 4. pii: btw379.

MetaQUAST: evaluation of metagenome assemblies.
Mikheenko A, Saveliev V, Gurevich A.
Bioinformatics. 2015 Nov 26. pii: btv697

Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi and Glenn Tesler
QUAST: quality assessment tool for genome assemblies
Bioinformatics volume 29, issue 8, pp. 1072-1075.

DNA Baser 4.36 – DNA Sequence Assembly & Analysis

DNA Baser 4.36

:: DESCRIPTION

DNA Baser is a tool for DNA sequence assembly, DNA sequence analysis, contig editing, and mutation detection. It also offers a powerful chromatogram viewer/editor.

::DEVELOPER

Heracle BioSoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DNA Baser

:: MORE INFORMATION

COCACOLA – Binning Metagenomic Contigs using Sequence COmposition, Read CoverAge, CO-alignment, and Paired-end Read LinkAge

COCACOLA

:: DESCRIPTION

COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs.

::DEVELOPER

COCACOLA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MatLab

:: DOWNLOAD

 COCACOLA

:: MORE INFORMATION

Citation

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge.
Lu YY, Chen T, Fuhrman JA, Sun F.
Bioinformatics. 2016 Jun 2. pii: btw290.

MaxBin 2.2 – Binning Assembled Metagenomic Sequences

MaxBin 2.2

:: DESCRIPTION

MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.

::DEVELOPER

The Joint BioEnergy Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MaxBin

:: MORE INFORMATION

Citation

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets.
Wu YW, Simmons BA, Singer SW.
Bioinformatics. 2015 Oct 29. pii: btv638.

GAML 0.1 – Genome Assembly by Maximum Likelihood

GAML 0.1

:: DESCRIPTION

GAML is a prototype genome assembly tool based on maximizing likelihood of the assembly in a model encompaasing error rate, insert length and other features of indvidual sequencing technologies.

:: DEVELOPER

Computational Biology @ Comenius University in Bratislava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GAML

:: MORE INFORMATION

Citation

GAML: genome assembly by maximum likelihood.
Boža V, Brejová B, Vinař T.
Algorithms Mol Biol. 2015 Jun 3;10:18. doi: 10.1186/s13015-015-0052-6.