SILP2 – ILP-based Maximum Likelihood Genome Scaffolding

SILP2

:: DESCRIPTION

SILP2 is a stand-alone scaffolding tool that generates maximum likelihood scaffolds via integer linear programming (ILP). SILP2 achieves high scalability without sacrificing optimality by solving the large ILP formulations required to scaffold mammalian-size genomes via a non-serial dynamic programming (NSDP) approach based on decomposing the scaffolding graph into 3-connected components.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SILP2

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014;15 Suppl 9:S9. doi: 10.1186/1471-2105-15-S9-S9. Epub 2014 Sep 10.
ILP-based maximum likelihood genome scaffolding.
Lindsay J, Salooti H, Măndoiu I, Zelikovsky A.

RaGOO v1.11 – Fast Reference-Guided Scaffolding of Genome Assembly Contigs

RaGOO v1.11

:: DESCRIPTION

RaGOO is a tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome.

::DEVELOPER

RaGOO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / OSX
Python

:: DOWNLOAD

RaGOO

:: MORE INFORMATION

Citation

RaGOO: fast and accurate reference-guided scaffolding of draft genomes.
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC.
Genome Biol. 2019 Oct 28;20(1):224. doi: 10.1186/s13059-019-1829-6.

SCUBAT – Scaffolding Contigs using BLAT and Transcripts

SCUBAT

:: DESCRIPTION

SCUBAT is a perl script uses any set of transcripts to identify cases where a transcript is split over multiple genome fragments and attempts to use this information to scaffold the genome.

::DEVELOPER

The Blaxter Lab at The Institute of Evolutionary Biology University of Edinburgh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
BLAT
CAP3
Perl

:: DOWNLOAD

SCUBAT

:: MORE INFORMATION