PaKman – Parallel Genome Assembler for Scalable Generation of Genomic Contigs

PaKman

:: DESCRIPTION

PaKman is a scalable algorithm for generating genomic contigs on distributed memory machines.

::DEVELOPER

Ananth Kalyanaraman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

PaKman

:: MORE INFORMATION

Citation

Ghosh, Priyanka, Sriram Krishnamoorthy, and Ananth Kalyanaraman.
“PaKman: A Scalable Algorithm for Generating Genomic Contigs on Distributed Memory Machines.”
IEEE Transactions on Parallel and Distributed Systems (TPDS) vol. 32, no. 5, pp. 1191-1209, 2021. DOI: 10.1109/TPDS.2020.3043241.

Varclus – Detection of Positive Selection in Genes and Genomes through Variation Clusters

Varclus

:: DESCRIPTION

Varclus is a perl utility to identify clusters of amino acid or nucleotide changes in a sequence that are too tightly spaced to have occurred by chance alone.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

 Varclus

:: MORE INFORMATION

Citation:

Wagner, A. (2007)
Rapid detection of positive selection in genes and genomes through variation clusters.
Genetics 176: 2451–2463

MAKER v3.01.03 – Genome Annotation pipeline

MAKER v3.01.03

:: DESCRIPTION

MAKER is a portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER’s inputs are minimal and its ouputs can be directly loaded into a GMOD database.

::DEVELOPER

Yandell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MAKER

:: MORE INFORMATION

Citation:

Genome Res. 2008 Jan;18(1):188-96. Epub 2007 Nov 19.
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M.

Genomer 0.1.0 – Genome Scaffolding

Genomer 0.1.0

:: DESCRIPTION

Genomer is command line glue for genome projects. It simplifies the small but tedious tasks required when finishing a genome. Genomer makes it easy to reorganise contigs in a genome, map annotations on to the genome and generate the files required to submit a genome.

:: DEVELOPER

Michael Barton

:: SCREENSHOTS

N/a

:: REQUIREMENTS

:: DOWNLOAD

 Genomer

 :: MORE INFORMATION

Citation

Genomer–a Swiss army knife for genome scaffolding.
Barton MD, Barton HA.
PLoS One. 2013 Jun 24;8(6):e66922. doi: 10.1371/journal.pone.0066922.

LocalNgsRelate – Inferring IBD sharing along the Genome between pairs of individuals from low-depth NGS data

LocalNgsRelate

:: DESCRIPTION

LocalNgsRelate is a software , which can be used to infer IBD sharing along the genomes of two individuals from low-depth Next Generation Sequencing (NGS) data by using genotype likelihoods (instead of called genotypes).

::DEVELOPER

LocalNgsRelate team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

LocalNgsRelate

:: MORE INFORMATION

Citation

Severson AL, Korneliussen TS, Moltke I.
LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data.
Bioinformatics. 2021 Oct 28:btab732. doi: 10.1093/bioinformatics/btab732. Epub ahead of print. PMID: 34718411.

genipe 1.5.0 – GENome-wide Imputation PipelinE

genipe 1.5.0

:: DESCRIPTION

The genipe module includes a script (named genipe-launcher) that automatically runs a genome-wide imputation pipeline using Plink, shapeit and impute2.

::DEVELOPER

Marie-Pierre Dubé’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Python

:: DOWNLOAD
enipe

:: MORE INFORMATION

Citation

Lemieux Perreault LP, Legault MA, Asselin G, Dubé MP.
genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools.
Bioinformatics. 2016 Dec 1;32(23):3661-3663. doi: 10.1093/bioinformatics/btw487. Epub 2016 Aug 6. PMID: 27497439; PMCID: PMC5181529.

GEDpm-cg – Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum

GEDpm-cg

:: DESCRIPTION

GEDpm-cg enables users to perform the efficient, automated and high-throughput design of single nucleotide editing in C. glutamicum chromosome. The counter-selection HR system and the overlap-based assembly method were chosen as the loading techniques. Homologous arms and primers required for genetic modification, vector DNA assembly and sequencing verification were provided as design results.

::DEVELOPER

Biodesign Centre, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web server
  • Python

:: DOWNLOAD

GEDpm-cg

:: MORE INFORMATION

Citation

Yang Y, Mao Y, Liu Y, Wang R, Lu H, Li H, Luo J, Wang M, Liao X, Ma H.
GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum.
Front Bioeng Biotechnol. 2021 Oct 15;9:768289. doi: 10.3389/fbioe.2021.768289. PMID: 34722482; PMCID: PMC8554027.

GMATA v2.3 – Genome-wide Microsatellite Analyzing Toward Application

GMATA v2.3

:: DESCRIPTION

GMATA is an easiest and fastest bioinformatic tool /software for any Simple Sequence Repeats (SSR) analyses, and SSR marker designing, polymorphism screen, and e-mapping in any DNA sequences.

::DEVELOPER

Xuewen Wang

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Perl

:: DOWNLOAD

GMATA

:: MORE INFORMATION

Citation

Wang X, Wang L.
GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing.
Front Plant Sci. 2016 Sep 13;7:1350. doi: 10.3389/fpls.2016.01350. PMID: 27679641; PMCID: PMC5020087.

GMATo 1.2 – Genome Microsatellite Analyzing Tool

GMATo 1.2

:: DESCRIPTION

GMATo is a novel soft for faster and accurate microsatellite mining at any length and comprehensive statistical analysis for DNA sequences in any genome at any size, with easily customized parameters control for biologists and bio-informatician, running easily at common computers with Windows, Linux, MAC OS etc multiple platforms (platform independently) with both graphic and command interface programmed in Java and Perl computing language.

::DEVELOPER

Xuewen Wang

:: SCREENSHOTS

GMATo

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Perl

:: DOWNLOAD

 GMATo

:: MORE INFORMATION

Citation

Bioinformation. 2013 Jun 8;9(10):541-4. doi: 10.6026/97320630009541. Print 2013.
GMATo: A novel tool for the identification and analysis of microsatellites in large genomes.
Wang X1, Lu P, Luo Z.

GGDC 3.0 – Genome-to-Genome Distance Calculator

GGDC 3.0

:: DESCRIPTION

GGDC  is an updated and enhanced version with improved DDH-prediction models and additional features such as confidence-interval estimation. To the best of our knowledge, it is the only digital DDH method that provides this feature. Of all genome-based methods we are aware of, GGDC 2.0 yields the highest correspondence to wet-lab DDH (without sharing DDH’s drawbacks).

::DEVELOPER

Leibniz Institute DSMZ

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Feb 21;14:60. doi: 10.1186/1471-2105-14-60.
Genome sequence-based species delimitation with confidence intervals and improved distance functions.
Meier-Kolthoff JP1, Auch AF, Klenk HP, Göker M.