Small manual

For this small demonstration, to run the GFinisher is necessary to obtain assemblies and a reference genome. In this case study, we use the assemblies provided by GAGE-B genome of Bacteroides fragilis - HiSeq.

The download of assemblies can be made of the GAGE-B site or sourceforge. The reference genome can be download from NCBI or here.

If your computer doesn't have Java installed, try to download java and install it (www.java.com), preferably the 64-bit version.

Download the GFinisher binaries link

With all the resources available for you to run GFinisher, get to run.

Graphics mode

Run GFinisher in system console:

java -Xms2G -Xmx4G -jar GenomeFinisher.jar

At tab "Blast" verify the path where the blast was installed.

 

Go back to "Basic" tab and choose msrca_ctg.fasta file to "Target assembly" field and click at "Add" button in alternative assemblies section and choose files: abyss_ctg.fasta, cabog_ctg.fasta, mira_ctg.fasta, sga_ctg.fasta, soap_ctg.fasta, spades_ctg.fasta, velvet_ctg.fasta.

Add FQ312004.fna file in reference genome.

The figure below shows the data setup.

Click the first button in main toolbar and wait for about 15 minutes.

Console/Text mode

Run GFinisher in system console:

 java -Xms2G -Xmx4G -jar GenomeFinisher.jar -config -create name_of_config.txt
            

Verify and adjust the settings on the name_of_config.txt, especially the path of the Blast and run

 java -Xms2G -Xmx4G -jar GenomeFinisher.jar -config name_of_config.txt -i msrca_ctg.fasta \
    -ref FQ312004.fna \
    -ds abyss_ctg.fasta,cabog_ctg.fasta,mira_ctg.fasta,sga_ctg.fasta,soap_ctg.fasta,spades_ctg.fasta,velvet_ctg.fasta \
    -o .\MaSuRCA\ -v 1

Results

When GFinisher is done all data generated stay at MaSuRCA folder. The table below show some reports produced by GFinisher in each steps. Click in image to expand view.

Report type	Original data	After contigSort	After Broken FGC Skew	Results
N. contigs	109	44	210	11
N. contigs (≥ 500bp)	109	44	210	11
N. contigs (≥ 1000bp)	102	44	210	11
N50	158716	309306	72014	663436
L50	11	6	23	3
Dotplot
GC Skew
Quast	report