Tag: Scaffold

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.

SALSA v2.3 – Scaffold long read Assemblies with Hi-C data

SALSA v2.3

:: DESCRIPTION

SALSA is a tool to scaffold long read assemblies with Hi-C.

::DEVELOPER

MarBL (Maryland Bioinformatics Labs)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SALSA

:: MORE INFORMATION

Citation

Ghurye J, Pop M, Koren S, Bickhart D, Chin CS.
Scaffolding of long read assemblies using long range contact information.
BMC Genomics. 2017 Jul 12;18(1):527. doi: 10.1186/s12864-017-3879-z. PMID: 28701198; PMCID: PMC5508778.

LongStitch v1.0.1 – Correct and Scaffold Assemblies using long Reads

LongStitch v1.0.1

:: DESCRIPTION

LongStitch is a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads.

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

LongStitch

:: MORE INFORMATION

Citation

Coombe L, Li JX, Lo T, Wong J, Nikolic V, Warren RL, Birol I.
LongStitch: high-quality genome assembly correction and scaffolding using long reads.
BMC Bioinformatics. 2021 Oct 30;22(1):534. doi: 10.1186/s12859-021-04451-7. PMID: 34717540.

L_RNA_scaffolder – Long Transcriptome Reads to Scaffold Genome

L_RNA_scaffolder

:: DESCRIPTION

L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to scaffold genome fragments.

::DEVELOPER

L_RNA_scaffolder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • Perl

:: DOWNLOAD

 L_RNA_scaffolder

:: MORE INFORMATION

Citation:

BMC Genomics. 2013 Sep 8;14:604. doi: 10.1186/1471-2164-14-604.
L_RNA_scaffolder: scaffolding genomes with transcripts.
Xue W1, Li JT, Zhu YP, Hou GY, Kong XF, Kuang YY, Sun XW.

SMAL – Scaffold-Based Multiple Network Aligner

SMAL

:: DESCRIPTION

The SMAL web-server is a public, open-source, web-based application for creating multiple network alignments (MNAs) from existing pairwise alignments (PNAs).

::DEVELOPER

Biocomputing and Media Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

The SMAL web server: global multiple network alignment from pairwise alignments.
Dohrmann J, Singh R.
Bioinformatics. 2016 Jul 4. pii: btw402.

GMcloser 1.6.2 / GMvalue 1.3 – Closing the Gaps in Scaffolds with Preassembled Contigs

GMcloser 1.6.2 / GMvalue 1.3

:: DESCRIPTION

GMcloser fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads.

GMvalue is a tool to determine misassembly sites in contigs and scaffolds.

::DEVELOPER

GMcloser team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GMcloser / GMvalue

:: MORE INFORMATION

Citation

GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments.
Kosugi S, Hirakawa H, Tabata S.
Bioinformatics. 2015 Aug 10. pii: btv465.

Atlas-Link 0.01 – Link Genome Sequence Contigs into Scaffold

Atlas-Link 0.01

:: DESCRIPTION

Atlas-Link links and orients genome sequence contigs into scaffolds quickly and accurately using mate-pair information. Atlas-Link can also be used to superscaffold existing genome assemblies with data from new sequencing technologies.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Atlas-Link

:: MORE INFORMATION

MIP Scaffolder 0.6 – Scaffold Contigs Produced by Fragment Assemblers

MIP Scaffolder 0.6

:: DESCRIPTION

MIP Scaffolder is a program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer.

::DEVELOPER

Leena Salmela

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MIP Scaffolder

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Dec 1;27(23):3259-65. Epub 2011 Oct 13.
Fast scaffolding with small independent mixed integer programs.
Salmela L, Mäkinen V, Välimäki, N, Ylinen J, Ukkonen E.

Scaffold-filling – Software for Filling the Scaffold

Scaffold-filling

:: DESCRIPTION

 Scaffold-filling inserts genes from a fully sequenced genome into predicted positions within the gaps of a genome with a lower quality assembly.

::DEVELOPER

Sankoff Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 Scaffold-filling

:: MORE INFORMATION

Citaion

Scaffold filling, contig fusion and comparative gene order inference.
Muñoz A, Zheng C, Zhu Q, Albert VA, Rounsley S, Sankoff D.
BMC Bioinformatics. 2010 Jun 4;11:304.

SOMA 2.0 – Scaffolding using Optical Restriction Mapping

SOMA 2.0

:: DESCRIPTION

SOMA (Scaffolding using Optical Restriction Mapping) is a toolbox for finishing a genome and moving it from a draft stage (the result of sequencing and initial assembly) to a complete genome. Optical Maps are global, ordered maps of restriction site locations in a genome. This information can be quite useful in scaffolding contigs from a shotgun assembly to guide the finishing process.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SOMA

:: MORE INFORMATION

N/A

 

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