Tag: Scaffolder

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.

ntJoin v1.0.8 – Genome Assembly Scaffolder using minimizer Graphs

ntJoin v1.0.8

:: DESCRIPTION

ntJoin is an assembly-guided scaffolder which uses a lightweight, alignment-free mapping strategy in lieu of alignments to quickly contiguate a target assembly using one or more

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

ntJoin

:: MORE INFORMATION

Citation

Coombe L, Nikolić V, Chu J, Birol I, Warren RL.
ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs.
Bioinformatics. 2020 Jun 1;36(12):3885-3887. doi: 10.1093/bioinformatics/btaa253. PMID: 32311025; PMCID: PMC7320612.

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