PyRAD 3.0.66 – Assembly of de novo RADseq loci for Phylogenetic Analyses

PyRAD 3.0.66

:: DESCRIPTION

PyRAD is a pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic datasets.

::DEVELOPER

Deren Eaton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 PyRAD

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 20.
PyRAD: assembly of de novo RADseq loci for phylogenetic analyses.
Eaton DA.

NovoHMM – hidden Markov model for de novo Peptide Sequencing

NovoHMM

:: DESCRIPTION

NovoHMM is a software for hidden Markov model for de novo peptide sequencing.

::DEVELOPER

Bernd Fischer

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 NovoHMM

:: MORE INFORMATION

Citation

Anal Chem. 2005 Nov 15;77(22):7265-73.
NovoHMM: a hidden Markov model for de novo peptide sequencing.
Fischer B, Roth V, Roos F, Grossmann J, Baginsky S, Widmayer P, Gruissem W, Buhmann JM.

mirTrios – Detection of de novo and rare inherited Mutations from Trios-based NGS

mirTrios

:: DESCRIPTION

mirTrios was developed for identification and comprehensive analysis the de novo and rare inherited variants with one or multiple trios samples based on high-throughput sequencing data starting from a VCF file (version 4). It uses reference gene definitions and hg19 genomic coordinates for annotation.

::DEVELOPER

mirTrios team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 N/A

:: MORE INFORMATION

Citation

mirTrios: an integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing.
Li J, Jiang Y, Wang T, Chen H, Xie Q, Shao Q, Ran X, Xia K, Sun ZS, Wu J.
J Med Genet. 2015 Apr;52(4):275-81. doi: 10.1136/jmedgenet-2014-102656.

OpenGrowth 1.0.1 – Construct de novo Ligands for Protein

OpenGrowth 1.0.1

:: DESCRIPTION

OpenGrowth is a research program which grows new ligands in proteins by connecting small organic fragments.

::DEVELOPER

The Shakhnovich Biophysics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux

:: DOWNLOAD

 OpenGrowth

:: MORE INFORMATION

Citation

OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands.
Chéron N, Jasty N, Shakhnovich EI.
J Med Chem. 2015 Sep 23

DNN-HMM – De novo Identification of Replication-timing Domains in the Human Genome

DNN-HMM

:: DESCRIPTION

DNN-HMM (deep neural network and a hidden Markov model) is a novel hybrid architecture combining a pre-trained,for the de novo identification of replication domains using replication timing profiles.

::DEVELOPER

DNN-HMM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab / Perl

:: DOWNLOAD

  DNN-HMM

:: MORE INFORMATION

Citation

De novo Identification of replication-timing domains in the human genome by deep learning.
Liu F, Ren C, Li H, Zhou P, Bo X, Shu W.
Bioinformatics. 2015 Nov 5. pii: btv643.

Telescoper 0.2 – De novo Assembly Algorithm

Telescoper 0.2

:: DESCRIPTION

Telescoper is a local assembly algorithm designed for short-reads from NGS platforms such as Illumina. The reads must come from two libraries: one short insert, and one long insert.

::DEVELOPER

Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Telescoper

:: MORE INFORMATION

Citation

Bresler, M., Sheehan, S., Chan, A.H., and Song, Y.S.
Telescoper: De novo Assembly of Highly Repetitive Regions.
Bioinformatics, 28 (2012) i311-i317.

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.

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)

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.

miniasm v0.3- Fast Overlapped-based de novo Assembler for Noisy long Reads

miniasm v0.3

:: DESCRIPTION

Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Miniasm

:: MORE INFORMATION

Citation

Li H.
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
Bioinformatics. 2016 Jul 15;32(14):2103-10. doi: 10.1093/bioinformatics/btw152. Epub 2016 Mar 19. PMID: 27153593; PMCID: PMC4937194.