MetaCarvel v1.1 – A Scaffolder for Metagenomes

MetaCarvel v1.1

:: DESCRIPTION

MetaCarvel is an updated version of previous metagenome scaffolder Bambus 2.

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

MetaCarvel

:: MORE INFORMATION

Citation:

Ghurye, J., Treangen, T., Fedarko, M., Hervey, W. J., & Pop, M. (2019).
MetaCarvel: linking assembly graph motifs to biological variants.
Genome biology, 20(1), 1-14.

MeDuSa 1.6 – Multi-draft based Scaffolder

MeDuSa 1.6

:: DESCRIPTION

MeDuSa (Multi-Draft based Scaffolder) is a draft genome scaffolder that uses multiple reference genomes in a graph-based approach.

::DEVELOPER

Florence Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • Java

:: DOWNLOAD

  MeDuSa

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Mar 25. pii: btv171.
MeDuSa: a multi-draft based scaffolder.
Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lió P, Crescenzi P, Fani R, Fondi M

GRASS 0.003 – GeneRic ASembly Scaffolder

GRASS 0.003

:: DESCRIPTION

GRASS is a generic algorithm for scaffolding next-generation sequencing assemblies.It offers a Mixed-Integer Programming (MIP) formulation of the contig sca olding problem, which com-bines contig order, distance and orientation in a single optimization objective. The resulting optimization problem is solved using an Expectation-Maximization procedure and an uncon-strained binary quadratic programming approximation of the original problem. Please refer to the original manuscript for details.

::DEVELOPER

The Delft Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GRASS

:: MORE INFORMATION