Tag: Hybrid

HASLR – Fast Hybrid Assembly of Long Reads

HASLR

:: DESCRIPTION

HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

HASLR

:: MORE INFORMATION

Citation

Haghshenas E, Asghari H, Stoye J, Chauve C, Hach F.
HASLR: Fast Hybrid Assembly of Long Reads.
iScience. 2020 Aug 21;23(8):101389. doi: 10.1016/j.isci.2020.101389. Epub 2020 Jul 25. PMID: 32781410; PMCID: PMC7419660.

HyAsP – Hybrid Assembler for Plasmids

HyAsP

:: DESCRIPTION

HyAsP is a tool for the extracting plasmids from WGS assemblies in an automatic way. It combines ideas from both reference-based and depth-based methods to identify plasmids in a greedy algorithm, using information on the occurrences of known plasmid genes and considering characteristics of the contigs such as read depth and GC content.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • conda

:: DOWNLOAD

HyAsP

:: MORE INFORMATION

Citation

Müller R, Chauve C.
HyAsP, a greedy tool for plasmids identification.
Bioinformatics. 2019 Nov 1;35(21):4436-4439. doi: 10.1093/bioinformatics/btz413. PMID: 31116364.

RHybridFinder 0.2.0 – Identification of Hybrid Peptides in Immunopeptidomic Analyses

RHybridFinder 0.2.0

:: DESCRIPTION

RHybridFinder (RHF) is an R package to process immunopeptidomic data for putative hybrid peptide discovery

::DEVELOPER

Frederic Saab <frederic.saab at umontreal.ca>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

RHybridFinder

:: MORE INFORMATION

Citation:

Saab F, Hamelin DJ, Ma Q, Kovalchik KA, Sirois I, Faridi P, Li C, Purcell AW, Kubiniok P, Caron E.
RHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery.
STAR Protoc. 2021 Oct 21;2(4):100875. doi: 10.1016/j.xpro.2021.100875. PMID: 34746858; PMCID: PMC8551247.

HRM – Hybrid Regulatory Models

HRM

:: DESCRIPTION

HRM is a general statistical inference framework for stochastic transcription-translation networks.

::DEVELOPER

Andrea Ocone ,Guido Sanguinetti

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • MatLab

:: DOWNLOAD

 HRM

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Apr 1;29(7):910-6. doi: 10.1093/bioinformatics/btt069. Epub 2013 Feb 13.
Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics.
Ocone A1, Millar AJ, Sanguinetti G.

HyDA 1.3.1 / Squeezambler 2.0.3 – Hybrid De Novo Assembler

HyDA 1.3.1 / Squeezambler 2.0.3

:: DESCRIPTION

HyDA is a multipurpose assembler, particularly tested for single cell and normal multicell genome co-assembly

Squeezambler is a divide-and-conquer algorithm for economical sequencing and assembly of all distinct genomes in a bacterial sample. The key idea here is exploiting sparsity, which is the small number of distinct genomes (~1000) in comparison to the huge number of cells (~100 trillion).

::DEVELOPER

Algorithmic Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HyDA / Squeezamler

:: MORE INFORMATION

Citation:

Narjes S. Movahedi, Elmirasadat Forouzmand, Hamidreza Chitsaz,
De Novo Co-assembly of Bacterial Genomes from Multiple Single Cells,
IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp 561-565, 2012

Bioinformatics. 2013 Aug 13. [Epub ahead of print]
Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities.
Taghavi Z, Movahedi NS, Draghici S, Chitsaz H.

HRSS 0.2 – Hybrid Relative Specificity Similarity based on Gene Ontology

HRSS 0.2

:: DESCRIPTION

HRSS provides a hybrid GO-based semantic similarity algorithm for evaluating the functional similarity between GO terms or gene products.

:: DEVELOPER

Center for Plant Environmental Sensing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MySQL

:: DOWNLOAD

 HRSS

:: MORE INFORMATION

Citation

Wu, X., Pang, E., Lin, K. and Pei, Z.M. (2013)
Improving the Measurement of Semantic Similarity between Gene Ontology Terms and Gene Products: Insights from an Edge- and IC-Based Hybrid Method.
PLoS One 8(5), e66745. doi:10.1371/journal.pone.0066745

HyDRA – Hybrid Distance-Score Rank Aggregation software for Gene Prioritization

HyDRA

:: DESCRIPTION

HyDRA is a new approach to genomic data aggregation which combines the advantages of score-based and combinatorial aggregation techniques.

::DEVELOPER

Olgica Milenkovic’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • MatLab

:: DOWNLOAD

 HyDRA

:: MORE INFORMATION

Citation

HyDRA: Gene Prioritization via Hybrid Distance-Score Rank Aggregation.
Kim M, Farnoud F, Milenkovic O.
Bioinformatics. 2014 Nov 18. pii: btu766.

RAPTR-SV 0.0.15 – Hybrid Method for Detection of Structural Variants

RAPTR-SV 0.0.15

:: DESCRIPTION

RAPTR-SV (ReAdPair spliT – Read Structural Variant) uses Read Pair and Split Read methods to identify structural variants in paired-end WGS data

::DEVELOPER

RAPTR-SV team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOSX
  • JDK for Java
  • MrsFAST

:: DOWNLOAD

 RAPTR-SV

:: MORE INFORMATION

Citation

RAPTR-SV: a hybrid method for the detection of structural variants.
Bickhart DM, Hutchison JL, Xu L, Schnabel RD, Taylor JF, Reecy JM, Schroeder S, Van Tassell CP, Sonstegard TS, Liu GE.
Bioinformatics. 2015 Feb 16. pii: btv086.

Cerulean 0.1.1 – Hybrid Genome Assembler

Cerulean 0.1.1

:: DESCRIPTION

Cerulean is a hybrid assembly using high throughput short and long reads

::DEVELOPER

Son K. Pham

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Cerulean

:: MORE INFORMATION

Citation

Viraj Deshpande, Eric DK Fung, Son Pham, Vineet Bafna,
Cerulean: A hybrid assembly using high throughput short and long reads (WABI2013)
rXiv preprint arXiv:1307.7933.

DanQ – A Hybrid Convolutional and Recurrent Neural Network for predicting the function of DNA Sequences

DanQ

:: DESCRIPTION

DanQ is a hybrid convolutional and recurrent neural network model for predicting the function of DNA de novo from sequence.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 DanQ

:: MORE INFORMATION

Citation

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.
Quang D, Xie X.
Nucleic Acids Res. 2016 Apr 15. pii: gkw226.

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