Tag: Contiguity

Binnacle – Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins

Binnacle

:: DESCRIPTION

binnacle is a tool for binning metagenomic datasets using assembly graphs and scaffolds generated by metacarvel.

::DEVELOPER

MarBL (Maryland Bioinformatics Labs)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

binnacle

:: MORE INFORMATION

Citation

Muralidharan HS, Shah N, Meisel JS, Pop M.
Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins.
Front Microbiol. 2021 Feb 24;12:638561. doi: 10.3389/fmicb.2021.638561. PMID: 33717033; PMCID: PMC7945042.

fragScaff – Genome Assembly with Contiguity Preserving Transposition

fragScaff

:: DESCRIPTION

FragScaff leverages coincidences between the content of different pools as a source of contiguity information for scaffolding de novo genome assemblies. FragScaff is complementary to Lachesis, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps.

::DEVELOPER

Shendure Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • Perl

:: DOWNLOAD

fragScaff

:: MORE INFORMATION

Citation

Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, Gunderson KL, Steemers FJ, Shendure J.
In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.
Genome Res. 2014 Dec;24(12):2041-9. doi: 10.1101/gr.178319.114. Epub 2014 Oct 19. PMID: 25327137; PMCID: PMC4248320.