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.

Phred/Phrap/Consed 29.0 – DNA Sequence Assembler & Finishing Tools

Phred/Phrap/Consed 29.0

:: DESCRIPTION

Phred reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.

phrap is a program for assembling shotgun DNA sequence data. Among other features, it allows use of the entire read and not just the trimmed high quality part, it uses a combination of user-supplied and internally computed data quality information to improve assembly accuracy in the presence of repeats, it constructs the contig sequence as a mosaic of the highest quality read segments rather than a consensus, it provides extensive assembly information to assist in trouble-shooting assembly problems, and it handles large datasets.

Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the user to pick primers and templates, suggesting additional sequencing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information.

::DEVELOPER

Laboratory of PHIL GREEN

:: SCREENSHOTS

:: REQUIREMENTS

Linux/Mac OsX

:: DOWNLOAD

Phred/Phrap/Consed

:: MORE INFORMATION

Citation:

Gordon, David. “Viewing and Editing Assembled Sequences Using Consed“, in Current Protocols in Bioinformatics,A. D. Baxevanis and D. B. Davison, eds, New York: John Wiley & Co., 2004, 11.2.1-11.2.43.
Gordon D, Desmarais C, Green P: Automated finishing with Autofinish. Genome Res 11:614-625 (2001).
Gordon D, Abajian C, Green P: Consed: a graphical tool for sequence finishing. Genome Research 8:195-202 (1998).

V-FAT 1.1 – Automated Finishing, Annotation, and QA tool for Viral Assemblies

V-FAT 1.1

:: DESCRIPTION

V-FAT (Viral Finishing and Annotation Toolkit) is a tool to perform automated computational finishing and annotation of de novo viral assemblies. V-FAT uses reference and read data to order and merge contigs, correct frameshifts, and produce NCBI-ready annotation files. It also performs a set of quality assurance measurements including coverage computation by gene or amplicon and identification of potential consensus errors.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

V-FAT

:: MORE INFORMATION

Citation

Charlebois, P, Yang, X, Newman, RM, Henn, MR, Zody, MC (2012)
V-FAT: a post-assembly pipeline for the finishing and annotation of viral genomes.
Submitted.