IMAP – Chromosome-level Genome Assembler Combining multiple de novo Assemblies

IMAP

:: DESCRIPTION

IMAP (the integrative meta-assembly pipeline) is a new software pipeline to build chromosome-level genome sequence assemblies by generating and combining multiple initial assemblies using three de novo assemblers from short-read sequencing data.

::DEVELOPER

Bioinformatics Laboratory, Konkuk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Java
Python
Perl

:: DOWNLOAD

IMAP

:: MORE INFORMATION

Citation

PLoS One. 2019 Aug 27;14(8):e0221858. doi: 10.1371/journal.pone.0221858. eCollection 2019.
Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies.
Song G, Lee J, Kim J, Kang S, Lee H, Kwon D, Lee D, Lang GI, Cherry JM, Kim J.

NucType 1.5 – Measure Distances/Size of Chromosomes and analysis Karyotype

NucType 1.5

:: DESCRIPTION

NucType is tool to measure distances/size of chromosomes, group the chromosomes and analysis the karyotype (karyotype asymmetry indices). Additionally it has a tool to measure the pollen or leaves.

::DEVELOPER

Yan Yu

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

NucType

:: MORE INFORMATION

3PD – Primer design for Chromosome Conformation Capture Assays

3PD

:: DESCRIPTION

3PD is a bioinformatics solution to support the experimentalist in detecting long-ranging intra or inter chromosomal contacts by Chromosome conformation capture (3C) assays.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Genomics. 2009 Dec 29;10:635. doi: 10.1186/1471-2164-10-635.
3PD: Rapid design of optimal primers for chromosome conformation capture assays.
Fröhler S, Dieterich C.

SCL 1.0 – Three-dimensional Chromosome Structures from Single-cell Hi-C data

SCL 1.0

:: DESCRIPTION

SCL (Single-Cell Lattice) is a computational method to reconstruct high-resolution 3D chromosome structures based on the zero-inflated single-cell Hi-C data.

::DEVELOPER

Z. WANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

SCL

:: MORE INFORMATION

Citation

Zhu H, Wang Z.
SCL: a lattice-based approach to infer 3D chromosome structures from single-cell Hi-C data.
Bioinformatics. 2019 Oct 15;35(20):3981-3988. doi: 10.1093/bioinformatics/btz181. PMID: 30865261; PMCID: PMC6792089.

HiCNet – Reconstruct High-resolution Chromosome 3D Structures based on Hi-C Complex Networks

HiCNet

:: DESCRIPTION

HiCNet is an approach for establishing small-world networks for individual chromosomes using Hi-C data. It is a tool capable of converting Hi-C contacts to spatial distances. And it can also infer three-dimensional structures using spatial distances and multidimensional scaling methods.

::DEVELOPER

Z. WANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

HiCNet

:: MORE INFORMATION

Citation

Liu T, Wang Z.
Reconstructing high-resolution chromosome three-dimensional structures by Hi-C complex networks.
BMC Bioinformatics. 2018 Dec 28;19(Suppl 17):496. doi: 10.1186/s12859-018-2464-z. PMID: 30591009; PMCID: PMC6309071.

3DChrom – Reconstruct Chromosome 3D Structures using Multidimensional Scaling

3DChrom

:: DESCRIPTION

Given a symmetric Hi-C contact matrix, 3DChrom can reconstruct three-dimensional (3D) structures of chromatins or topologically associating domains (TADs)

::DEVELOPER

Z. WANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Liu T, Wang Z.
Exploring the 2D and 3D structural properties of topologically associating domains.
BMC Bioinformatics. 2019 Dec 2;20(Suppl 16):592. doi: 10.1186/s12859-019-3083-z. PMID: 31787081; PMCID: PMC6886161.

AgileSamFileSorter 20120105 – Ordering Sequence Reads in a *.sam file by Chromosome and Map Position

AgileSamFileSorter 20120105

:: DESCRIPTION

AgileSAMFileSorter reads the sequence reads in an unsorted *.sam file and creates a second *.sam file in which all the sequence reads are sorted by chromosome number and position.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

Windows
Microsoft .NET framework version 2.0

:: DOWNLOAD

AgileSamFileSorter

:: MORE INFORMATION

ChromSDE 2.2 – Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C Data

ChromSDE 2.2

:: DESCRIPTION

ChromSDE is a deterministic method , which applies semi-definite programming techniques to find the best structure fitting the observed data and uses golden section search to find the correct parameter for converting the contact frequency to spatial distance.

::DEVELOPER

Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
MatLab

:: DOWNLOAD

ChromSDE

:: MORE INFORMATION

Citation

J Comput Biol. 2013 Nov;20(11):831-46. doi: 10.1089/cmb.2013.0076.
3D chromosome modeling with semi-definite programming and Hi-C data.
Zhang Z, Li G, Toh KC, Sung WK.

NEMO 1.5.2 – Analyzing Gene and Chromosome Territory Distributions from 3D-FISH Experiments

NEMO 1.5.2

:: DESCRIPTION

NEMO is a new Smart 3D-FISH (Three-dimensional fluorescence in situ hybridization) graphical user interface which provides all information in the same place so that results can be checked and validated efficiently.

::DEVELOPER

NEMO team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOsX
Java
ImageJ

:: DOWNLOAD

NEMO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Mar 1;26(5):696-7. doi: 10.1093/bioinformatics/btq013. Epub 2010 Jan 14.
NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments.
Iannuccelli E1, Mompart F, Gellin J, Lahbib-Mansais Y, Yerle M, Boudier T.

Gen3D – 3D Genome and Chromosome Structural Model Construction

Gen3D

:: DESCRIPTION

Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations.

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

Gen3D

:: MORE INFORMATION

Citation

Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data.
Nowotny J, Ahmed S, Xu L, Oluwadare O, Chen H, Hensley N, Trieu T, Cao R, Cheng J.
BMC Bioinformatics. 2015 Oct 23;16(1):338.