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.

ARCS / ARKS v1.2.2 – Genome Assembly Scaffolder with linked and Long Reads

ARCS / ARKS v1.2.2

:: DESCRIPTION

ARCS is a genomics software for scaffolding genome assembly drafts using linked or long reads.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ARCS

:: MORE INFORMATION

Citation

Coombe L, Zhang J, Vandervalk BP, Chu J, Jackman SD, Birol I, Warren RL.
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.
BMC Bioinformatics. 2018 Jun 20;19(1):234. doi: 10.1186/s12859-018-2243-x. PMID: 29925315; PMCID: PMC6011487.

JAGuaR 2.1 – Junction Alignment to Genome for Repositioning RNA-seq Reads

JAGuaR 2.1

:: DESCRIPTION

JAGuaR is an alignment protocol for paired end RNA-seq reads based on an extended reference.  It uses BWA to align reads to the genome and reference transcript models (including annotated exon-exon junctions) specifically allowing the possibility for a single read to span multiple exons.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

  JAGuaR

:: MORE INFORMATION

Citation

Butterfield YS, Kreitzman M, Thiessen N, Corbett RD, Li Y, Pang J, Ma YP, Jones SJ, Birol İ.
JAGuaR: junction alignments to genome for RNA-seq reads.
PLoS One. 2014 Jul 25;9(7):e102398. doi: 10.1371/journal.pone.0102398. PMID: 25062255; PMCID: PMC4111418.

ntEdit v1.3.5 – Ultra Fast and Scalable Genome Assembly Polishing

ntEdit v1.3.5

:: DESCRIPTION

ntEdit is a fast and scalable genomics application for polishing genome assembly drafts and other sequences.

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ntEdit

:: MORE INFORMATION

Citation

Warren RL, Coombe L, Mohamadi H, Zhang J, Jaquish B, Isabel N, Jones SJM, Bousquet J, Bohlmann J, Birol I.
ntEdit: scalable genome sequence polishing.
Bioinformatics. 2019 Nov 1;35(21):4430-4432. doi: 10.1093/bioinformatics/btz400. PMID: 31095290; PMCID: PMC6821332.