CONTIGuator 2.7.5 – Bacterial Genomes Finishing tool for Structural Insights on Draft Genomes

CONTIGuator 2.7.5

:: DESCRIPTION

CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome finshing process, taking advantage of the high number of near genomes that can be used to align and resolve the relative position of the contigs obtained with the latest sequencing technologies and therefore to design a set of PCR primers in order to fill the gaps and take a step further in the finishing process. It also can be used to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).

::DEVELOPER

Florence Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 CONTIGuator

:: MORE INFORMATION

Citation

Source Code Biol Med. 2011 Jun 21;6:11. doi: 10.1186/1751-0473-6-11.
CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes.
Galardini M, Biondi EG, Bazzicalupo M, Mengoni A.

ACCUSA 20140930 / ACCUSA2 – (Multi-purpose) SNP Calling on Draft Genomes

ACCUSA 20140930 / ACCUSA2

:: DESCRIPTION

ACCUSA is designed for accurate SNP calling on draft genome sequences.The main objective is to rule out pseudo SNPs where the reference genome has low sequencing base quality. This is obtained using a Bayesian framework considering the base quality values of the resequencing reads as well as the base quality of the reference genome.

ACCUSA2: Multi-purpose SNV calling enhanced by probabilistic integration of quality scores

::DEVELOPER

BIMSB Bioinformatics Core.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java 

:: DOWNLOAD

  ACCUSA , ACCUSA2

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 May 15;26(10):1364-5. Epub 2010 Apr 1.
ACCUSA–accurate SNP calling on draft genomes.
Fröhler S, Dieterich C.

Bioinformatics. 2013 Jul 15;29(14):1809-10. doi: 10.1093/bioinformatics/btt268. Epub 2013 May 16.
ACCUSA2: multi-purpose SNV calling enhanced by probabilistic integration of quality scores.
Piechotta M, Dieterich C.

misSEQuel v1.0beta – Misassembly Detection in Draft Genomes

misSEQuel v1.0beta

:: DESCRIPTION

misSEQuel is a software that enhances the quality of draft genomes by identifying misassembly errors and their breakpoints using paired-end sequence reads and optical mapping data.

::DEVELOPER

SEQ Development Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • Python
  • TWIN
  • BWA

:: DOWNLOAD

 misSEQuel

:: MORE INFORMATION

Citation

Misassembly detection using paired-end sequence reads and optical mapping data.
Muggli MD, Puglisi SJ, Ronen R, Boucher C.
Bioinformatics. 2015 Jun 15;31(12):i80-i88. doi: 10.1093/bioinformatics/btv262

RepeatFinder – Finding Repetitive Sequences Complete and Draft Genomes

RepeatFinder

:: DESCRIPTION

RepeatFinder is a system for finding and characterizing repetitive sequences in complete and partial genomes.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RepeatFinder

:: MORE INFORMATION

Citation:

Genome Biol. 2001;2(8):RESEARCH0027. Epub 2001 Aug 1.
A clustering method for repeat analysis in DNA sequences.
Volfovsky N, Haas BJ, Salzberg SL.