Tag: Scaffolding

ADseq – Comparative Scaffolding

ADseq

:: DESCRIPTION

ADseq is a new method, that allows to improve scaffolding of extant genomes and jointly reconstructs gene order in ancestral genomes.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ADseq

:: MORE INFORMATION

Citation

Anselmetti Y, Duchemin W, Tannier E, Chauve C, Bérard S.
Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.
BMC Genomics. 2018 May 9;19(Suppl 2):96. doi: 10.1186/s12864-018-4466-7. PMID: 29764366; PMCID: PMC5954271.

Genomer 0.1.0 – Genome Scaffolding

Genomer 0.1.0

:: DESCRIPTION

Genomer is command line glue for genome projects. It simplifies the small but tedious tasks required when finishing a genome. Genomer makes it easy to reorganise contigs in a genome, map annotations on to the genome and generate the files required to submit a genome.

:: DEVELOPER

Michael Barton

:: SCREENSHOTS

N/a

:: REQUIREMENTS

:: DOWNLOAD

 Genomer

 :: MORE INFORMATION

Citation

Genomer–a Swiss army knife for genome scaffolding.
Barton MD, Barton HA.
PLoS One. 2013 Jun 24;8(6):e66922. doi: 10.1371/journal.pone.0066922.

CSAR / Multi-CSAR – Contig Scaffolding tool using Algebraic Rearrangements

CSAR / Multi-CSAR

:: DESCRIPTION

CSAR is a contig scaffolding tool that can efficiently and accurately scaffold the contigs of a draft genome (i.e., target genome) based on an incomplete reference genome of a related organism.

Multi-CSAR is a multiple reference-based contig scaffolder using algebraic rearrangements

::DEVELOPER

Chin Lung Lu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • PHP

:: DOWNLOAD

CSAR / Multi-CSAR

:: MORE INFORMATION

Citation

Chen KT, Shen HT, Lu CL.
Multi-CSAR: a multiple reference-based contig scaffolder using algebraic rearrangements.
BMC Syst Biol. 2018 Dec 31;12(Suppl 9):139. doi: 10.1186/s12918-018-0654-y. PMID: 30598087; PMCID: PMC6311912.

Chen KT, Lu CL.
CSAR-web: a web server of contig scaffolding using algebraic rearrangements.
Nucleic Acids Res. 2018 Jul 2;46(W1):W55-W59. doi: 10.1093/nar/gky337. PMID: 29733393; PMCID: PMC6030906.

Chen KT, Liu CL, Huang SH, Shen HT, Shieh YK, Chiu HT, Lu CL.
CSAR: a contig scaffolding tool using algebraic rearrangements.
Bioinformatics. 2018 Jan 1;34(1):109-111. doi: 10.1093/bioinformatics/btx543. PMID: 28968788.

OMGS – Optical Map-Based Genome Scaffolding

OMGS

:: DESCRIPTION

OMGS is a fast genome scaffolding tool which takes advantage of one or multiple Bionano optical maps to accurately generate scaffolds.

::DEVELOPER

Weihua Pan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

OMGS

:: MORE INFORMATION

Citation

Pan W, Jiang T, Lonardi S.
OMGS: Optical Map-Based Genome Scaffolding.
J Comput Biol. 2020 Apr;27(4):519-533. doi: 10.1089/cmb.2019.0310. Epub 2019 Dec 3. PMID: 31794680.

SLiQ – Simple linear Inequalities based Mate-Pair reads Filtering and Scaffolding

SLiQ

:: DESCRIPTION

SLIQ , a set of simple linear inequalities derived from the geometry of contigs on the line, can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph.

::DEVELOPER

Schliep lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Mac OsX / Windows
  • Python

:: DOWNLOAD

 SLiQ 

:: MORE INFORMATION

Citation

SLIQ: simple linear inequalities for efficient contig scaffolding.
Roy RS, Chen KC, Sengupta AM, Schliep A.
J Comput Biol. 2012 Oct;19(10):1162-75.

ScaffMatch 0.9 – Scaffolding Algorirthm Based on Maximum Weight Matching

ScaffMatch v0.9

:: DESCRIPTION

ScaffMatch is a novel scaffolding tool based on Maximum-Weight Matching able to produce high-quality scaffolds from NGS data (reads and contigs).

::DEVELOPER

Georgia State University NGS Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 ScaffMatch

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Apr 17. pii: btv211.
ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching.
Mandric I, Zelikovsky A

Rascaf v1.0.2 – Scaffolding with RNA-seq Read Alignment

Rascaf v1.0.2

:: DESCRIPTION

Rascaf (RnA-seq SCAFfolder) uses continuity and order information from paired-end RNA-seq reads to improve a draft assembly, particularly in the gene regions. It takes as input an assembly and one or several RNA-seq data sets aligned to the genome, and recruits additional contigs into the assembly, potentially adjusting some scaffolds to better fit the data and to create longer gene models.

::DEVELOPER

Li Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsx/Linux

:: DOWNLOAD

Rascaf

:: MORE INFORMATION

Citation

Song L, Shankar DS, Florea L.
Rascaf: Improving Genome Assembly with RNA Sequencing Data.
Plant Genome. 2016 Nov;9(3). doi: 10.3835/plantgenome2016.03.0027. PMID: 27902792.

TransPS 1.1.0 – Transcriptome Post Scaffolding

TransPS 1.1.0

:: DESCRIPTION

TransPS is a pipeline for post-processing of pre-assembled transcriptomes using reference based method.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 TransPS

:: MORE INFORMATION

Citation

A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs,
Computational Biology Journal, vol. 2014, Article ID 961823, 4 pages, 2014. doi:10.1155/2014/961823
Mingming Liu, Zach N. Adelman, Kevin M. Myles, and Liqing Zhang

SWALO – Scaffolding with Assembly Likelihood Optimization

SWALO

:: DESCRIPTION

SWALO is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing.

::DEVELOPER

Pachter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  •  Bowtie 2

:: DOWNLOAD

SWALO

:: MORE INFORMATION

 

scarpa 0.241 – Scaffolding Reads with Practical Algorithms

scarpa 0.241

:: DESCRIPTION

Scarpa is a stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data.

::DEVELOPER

Nilgun Donmez and Michael Brudno

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 scarpa

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):428-34. doi: 10.1093/bioinformatics/bts716. Epub 2012 Dec 29.
SCARPA: scaffolding reads with practical algorithms.
Donmez N, Brudno M.