DNMFilter 0.1.1 – De Novo Mutation Filter

DNMFilter 0.1.1

:: DESCRIPTION

DNMFilter is a machine learning based tool designed to filter out false positive de novo mutations (DNMs) obtained by any computational or manual approaches from next generation sequencing data.

::DEVELOPER

DNMFilter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Python

:: DOWNLOAD

 DNMFilter

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 27.
A gradient-boosting approach for filtering de novo mutations in parent-offspring trios.
Liu Y1, Li B, Tan R, Zhu X, Wang Y.

BinPacker 1.1 – Packing-Based De Novo Transcriptome Assembly from RNA-seq Data

BinPacker 1.1

:: DESCRIPTION

BinPacker is a novel de novo assembler by modeling the transcriptome assembly problem as tracking a set of trajectories of items with their sizes representing coverage of their corresponding isoforms by solving a series of bin-packing problems.

::DEVELOPER

BinPacker team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BinPacker

:: MORE INFORMATION

Citation

BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data.
Liu J, Li G, Chang Z, Yu T, Liu B, McMullen R, Chen P, Huang X.
PLoS Comput Biol. 2016 Feb 19;12(2):e1004772. doi: 10.1371/journal.pcbi.1004772.

W-ChIPMotifs – de novo Motif Discovery from ChIP-based High throughput data

W-ChIPMotifs

:: DESCRIPTION

W-ChIPMotifs is a web application tool for de novo motif discovery from ChIP-based high throughput data.

::DEVELOPER

Jin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data.
Jin VX, Apostolos J, Nagisetty NS, Farnham PJ.
Bioinformatics. 2009 Dec 1;25(23):3191-3.

LTRsift 1.0.2 – Postprocessing of de novo predicted LTR Retrotransposon Annotations

LTRsift 1.0.2

:: DESCRIPTION

LTRsift is a graphical desktop tool for semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations, such as the ones generated by LTRharvest and LTRdigest.

::DEVELOPER

RESEARCH GROUP FOR GENOME INFORMATICS ,Center for Bioinformatics, University of Hamburg

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

LTRsift

:: MORE INFORMATION

Citation:

S. Steinbiss, S. Kastens and S. Kurtz:
LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.
Mobile DNA, 3:18 (2012)

TGNet – Visualization and Quality Assessment of de novo Genome Assemblies

TGNet

:: DESCRIPTION

TGNet is a Cytoscape-based tool for visualization and quality assessment of de novo genome assemblies. Specifically it facilitates rapid detection of inconsistencies between a genome assembly and an independently derived transcriptome assembly.

::DEVELOPER

Wurm Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • Cytoscape

:: DOWNLOAD

 TGNet

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Dec 15;27(24):3425-6. doi: 10.1093/bioinformatics/btr569. Epub 2011 Oct 12.
Visualization and quality assessment of de novo genome assemblies.
Riba-Grognuz O, Keller L, Falquet L, Xenarios I, Wurm Y.

Rnnotator 3.5.0 – de novo Transcriptome Assembly pipeline from stranded RNA-Seq reads

Rnnotator 3.5.0

:: DESCRIPTION

Rnnotator is an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome.

::DEVELOPER

Zhong Wang at U.S. Department of Energy Joint Genome Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • BioPerl
  • Blat

:: DOWNLOAD

  Rnnotator

:: MORE INFORMATION

Citation

BMC Genomics. 2010 Nov 24;11:663. doi: 10.1186/1471-2164-11-663.
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z.

DETONATE 1.10 – DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation

DETONATE 1.10

:: DESCRIPTION

DETONATE consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.

::DEVELOPER

Colin Dewey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DETONATE

:: MORE INFORMATION

Citation

Genome Biol. 2014 Dec 21;15(12):553. doi: 10.1186/s13059-014-0553-5.
Evaluation of de novo transcriptome assemblies from RNA-Seq data.
Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN.

A5-miseq 20150522 – de novo Assembly & Analysis of Illumina Sequence data

A5-miseq 20150522

:: DESCRIPTION

de novo assembly & analysis of Illumina sequence data, including the A5 pipeline, A5-miseq, tools to evaluate assembly quality, and scripts to facilitate data submission to NCBI and the RAST annotation system

::DEVELOPER

A5-miseq team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 A5-miseq

:: MORE INFORMATION

Citation

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.
Coil D, Jospin G, Darling AE.
Bioinformatics. 2014 Oct 22. pii: btu661.

ABySS 1.9.0 – de novo, parallel, paired-end Sequence Assembler

ABySS 1.9.0

:: DESCRIPTION

ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

::DEVELOPER

Shaun Jackman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 ABySS

:: MORE INFORMATION

Citation

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.
ABySS: A parallel assembler for short read sequence data.
Genome Res. 2009. 19: 1117-1123

HHrepID 1.0.0 – de novo Protein Repeat Detection

HHrepID 1.0.0

:: DESCRIPTION

HHrepID is a novel automated procedure for the de novo identification of repeats in protein sequences. It is able to detect the sequence signature of structural repeats in many proteins that have not yet been known to possess internal sequence symmetry, such as TIM barrels and outer membrane beta-barrels. HHrepID uses HMM-HMM comparison to exploit evolutionary information in the form of the multiple sequence alignment of homologs, but in contrast to HHrep, the new method has several novel characteristics: (1) automated generation of a multiple alignment of repeats; (2) utilization of the transitive nature of homology through a novel merging procedure based on the fully probabilistic treatment of alignments; (3) superior alignment quality through an algorithm that maximizes the expected accuracy of an alignment; (4) the ability to identify different repeats within complicated architectures or multiple domains through automatic domain boundary detection, (5) new statistical treatment yielding improved sensitivity.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  HHrepID

:: MORE INFORMATION

Citation

Biegert A, Söding J:
HHrepID: de novo protein repeat identification by probabilistic consistency
Bioinformatics 2008 24(6), 807-814.