Tag: Contig

Tracembler – Contig Assembly Tool

Tracembler

:: DESCRIPTION

Tracembler takes one or multiple DNA or protein sequence(s) as input to the NCBI Trace Archive BLAST engine to identify matching sequence reads from a species of interest. The BLAST searches are carried out recursively such that BLAST matching sequences identified in previous rounds of searches are used as new queries in subsequent rounds of BLAST searches. Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads.

::DEVELOPER

The Brendel Group @ Indiana University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Tracembler

:: MORE INFORMATION

Citation

Dong, Q., Wilkerson, M.D. & Brendel, V. (2007)
Tracembler – software for in silico chromosome walking in unassembled genomes.
BMC Bioinformatics 8, 151.

CAT/BAT v5.2.3 – Taxonomic Classification of Contigs and Metagenome-assembled Genomes

CAT/BAT v5.2.3

:: DESCRIPTION

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies.

::DEVELOPER

Bas E. Dutilh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

CAT/BAT

:: MORE INFORMATION

Citation

von Meijenfeldt FAB, Arkhipova K, Cambuy DD, Coutinho FH, Dutilh BE.
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT.
Genome Biol. 2019 Oct 22;20(1):217. doi: 10.1186/s13059-019-1817-x. PMID: 31640809; PMCID: PMC6805573.

G4ALL 1.1 – Graphic Contig Analyzer for All Sequencing Platforms

G4ALL 1.1

:: DESCRIPTION

G4ALL is a stand-alone tool that facilitates the editing of the contigs generated by assembly process. G4ALL use mapping results produced by Blast or Mummer against a reference genome to generate a scaffold based on the overlap of the contigs after curation. Besides providing information on the gene products contained in each contig, obtained through a search of the available biological databases which can be inserted in G4ALL database.

::DEVELOPER

Dr. Rommel Ramos – rommelramos@ufpa.br

:: SCREENSHOTS

G4ALL

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 G4ALL

:: MORE INFORMATION

Citation

Bioinformation. 2013 Jun 29;9(11):599-604. doi: 10.6026/97320630009599. Print 2013.
Graphical contig analyzer for all sequencing platforms (G4ALL): a new stand-alone tool for finishing and draft generation of bacterial genomes.
Ramos RT1, Carneiro AR, Caracciolo PH, Azevedo V, Schneider MP, Barh D, Silva A.

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.

CAR – Contig Assembly of Prokaryotic Draft Genomes Using Rearrangements

CAR

:: DESCRIPTION

CAR is an efficient and more accurate tool for assembling contigs of a prokaryotic draft genome based on a reference genome.

::DEVELOPER

Chin Lung Lu,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

No

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Nov 28;15(1):381.
CAR: contig assembly of prokaryotic draft genomes using rearrangements.
Lu C, Chen KT, Huang SY, Chiu HT.

SuRankCo R5 – Supervised Ranking of Contigs in de novo Assemblies

SuRankCo R5

:: DESCRIPTION

SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet.

::DEVELOPER

SuRankCo team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java
  • R

:: DOWNLOAD

SuRankCo

:: MORE INFORMATION

Citation

Kuhring M, Dabrowski PW, Piro VC, Nitsche A, Renard BY.
SuRankCo: supervised ranking of contigs in de novo assemblies.
BMC Bioinformatics. 2015 Jul 30;16:240. doi: 10.1186/s12859-015-0644-7. PMID: 26224355; PMCID: PMC4520199.

SimAssemblyStage1/2 0.2 – Assembly Alignment of Contigs

SimAssemblyStage1/2 0.2

:: DESCRIPTION

SimAssemblyStage1: Perfectly aligns TranscriptSimulator reads to their nucleotide templates using read title inforamation, creating ideal simulated assembly of super contigs.

SimAssemblyStage2: Creates an optimal simulated assembly alignment of contigs using the output of SimAssemblyStage1.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SimAssemblyStage1/2

:: MORE INFORMATION

ScaffoldScaffolder 0.1 – Solving Contig Orientation via Bidirected to Directed Graph Reduction

ScaffoldScaffolder 0.1

:: DESCRIPTION

ScaffoldScaffolder is a stand-alone scaffolding algorithm which was designed specifically for scaffolding diploid genomes.

::DEVELOPER

Computational Science Laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JAVA

:: DOWNLOAD

 ScaffoldScaffolder

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2015;16 Suppl 7:S5. doi: 10.1186/1471-2105-16-S7-S5. Epub 2015 Apr 23.
Heterozygous genome assembly via binary classification of homologous sequence.
Bodily PM, Fujimoto M, Ortega C, Okuda N, Price JC, Clement MJ, Snell Q.

ScaffoldScaffolder: Solving Contig Orientation via Bidirected to Directed Graph Reduction.
Bodily PM, Fujimoto MS, Snell Q, Ventura D, Clement MJ.
Bioinformatics. 2015 Sep 17. pii: btv548.

ESTminer 1.0 – Mining EST Contig and Cluster databases

ESTminer 1.0

:: DESCRIPTION

ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster data sets.  The Web interface contains a query frame that allows the selection of contigs/clusters with specific cDNA library makeup or threshold number of members with the results displayed as color-coded tree nodes where the color indicats the fractional size of each cDNA library component.  The nodes are expandable, revealing library statistics as well as EST or contig members with links that can be configured for sequence data, GenBank records, or other user configurable links.  Also, the interface allows “queries within queries” where the result set of a query is further filtered by the subsequent query.

::DEVELOPER

ESTminer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • JAKARTA TOMCAT
  • MySQL

:: DOWNLOAD

  ESTminer

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Mar 1;21(5):669-70.
ESTminer: a Web interface for mining EST contig and cluster databases.
Huang Y, Pumphrey J, Gingle AR.