GFinisher. bioinformatics tool developed in the Graduate Program in Sciences - Biochemistry at the UFPR

GFinisher - Genome Finisher

Easy and rapid to improve, refine and close your genome assembly.

GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references.

Requirements

Data

Two or more de novo assemblies.
One genome reference.

Resource

NCBI Blast 2.2.29+ (or higher)

Enviroment

GFinisher developed in java plataform, you can use in most operating systems.

For the assembly of bacterial organisms, we observed a memory consumption of about 4Gb RAM.

Java Virtual Machine required (version 7 or up)

GFinisher requires and include jFreeChart library

Open-source

GFinisher is open-source, you can use, modify and redistribute freely.

BSD license like

How to

manual will soon be available

basic purposes

  java -Xms2G -Xmx4G -jar GenomeFinisher.jar  \
    -i target_contigs.fasta  \
    -ds alternative_assemblies.fasta -ref reference.fasta  \
    -o outputDirectory

Generate the template configuration file

  java -jar GenomeFinisher.jar -config -create config.txt

running with the configuration file

  java -Xms2G -Xmx4G -jar GenomeFinisher.jar \
    -i target_contigs.fasta -ds alternative_assemblies.fasta -ref reference.fasta \
    -o outputDirectory -config config.txt

To extend the reports

  java -Xms2G -Xmx4G -jar GenomeFinisher.jar -i target_contigs.fasta  \
    -ds alternative_assemblies.fasta -ref reference.fasta -o outputDirectory  \
    -v 3

Default language

  java -Xms2g -Xmx4g -Duser.language=en -jar GenomeFinisher.jar

News and Updates

Here you will find release notes and news related to GFinisher.

2016-sep-19

version 1.4 - bug fixed - blast path on linux.

2016-jun-17

version 1.3 - bug fixed - blast configuration.

2016-jun-13

version 1.2 - binaries, source and site updated.

2016-may-13

version 1.1 - fix bug unknow symbols.

2016-may-06

version 1.0 launched - binaries, source and site published.

References

Guizelini, Dieval; Raittz, Roberto T.; Cruz, Leonardo M.; Souza, Emanuel M.; Steffens, Maria B. R.; Pedrosa, Fabio O. GFinisher : a new strategy to refine and finish bacterial genome assemblies. Scientific Reports 6, 1-8 (2016). URL http://dx.doi.org/10.1038/srep34963.

Link: Scientific Reports http://www.nature.com/articles/srep34963

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