ProDeGe: a computational protocol for fully automated decontamination of genomes

Dear All:

I want to use the tool "ProDeGe: a computational protocol for fully automated decontamination of genomes". Any of you has used before?

http://jgi.doe.gov/automating-microbial-genome-sequence-decontamination/

I tried to find a manual, but I could not. I need an explanation about how to use.

Thank you.

rna-seq next-gen alignment

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written 9.7 years ago by Mehmet

I'm familiar with it, but have not personally used it. Can you describe the project you are working on and the type of contamination you are experiencing?

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written 9.7 years ago by Brian Bushnell

hi; I am working on a worm project. I have its transcriptome data. I would like to check whether the data is contaminated by bacteria or not. I want to know how to do this by prodege. I need a step by step explanation.

Thank you.

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written 9.7 years ago by Mehmet

Everyone at JGI is on vacation because it's Thanksgiving, but on Monday I can talk to the people who use it routinely.

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written 9.7 years ago by Brian Bushnell

Why not use bbsplit with worm reference. That should leave all non-worm reads behind. Check the reads with blast afterwards.

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written 9.7 years ago by GenoMax

Dear Brian:

I got the program from my supervisor. Can I ask you a few questions about the program?

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written 9.7 years ago by Mehmet

You can certainly ask, but like I said, I have never used it, I only work with people who use it. I know a little about how it works, though.

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written 9.7 years ago by Brian Bushnell

OK.

the program needs a configuration file, as it is suggested in README file.

I am pasting here: INPUT/OUTPUT ProDeGe takes as input a fasta file that includes contigs from contaminant origin and the taxonomy of the target organism, and creates a fasta file including only the contigs from the target organism. Several intermediary files are created during the process.

RUNNING prodege.sh <configuration file="">

EXAMPLE Two examples are included in the Examples folder. The config.cfg needs to be updated with the install location and the working directory. To run the example type: prodege.sh <config file="">

My questions are:

Should I create a configuration file in which I have to write bacteria names that I want to check in my transcriptome data?If yes, can I write general bacteria names?

I need help about how to run this analysis.

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written 9.7 years ago by Mehmet

CONFIGURATION
The program takes as input a configuration file. Below are the fields that should be in the file:
TAXON_DISPLAY_NAME=         # This field is not required, put quotes around if spaces
TAXON_DOMAIN=               # Put quotes around taxon var assignments
TAXON_PHYLUM=               # because some have spaces in them
TAXON_CLASS=                # like "Bacteroidetes/Chlorobi group"
TAXON_ORDER=                # TAXON_X can be blank
TAXON_FAMILY=
TAXON_GENUS=            
INSTALL_LOCATION=           # Do not set this if you are using 'module load prodege'
WORKING_DIR=                # Prodege will create a folder $JOB_NAME in $WORKING_DIR
IN_FASTA=           # Full path of input fna
JOB_NAME=                   # Clean fasta file will be: ${WORKING_DIR}/${JOB_NAME}/${JOB_NAME}_output_clean.fna
RUN_GENECALL=<0 to skip, 1 to run>
RUN_BLAST=<0 to skip, 1 to run>
RUN_CLASSIFY=<0 to skip, 1 to run>
RUN_ACCURACY=<0 to skip, 1 to run>  #contigs must have "clean" or "contam" in their fasta's contig name
BLAST_THREADS=                      #Default is 8 
KMER_CUTOFF=                #Prodege is precalibrated with a cutoff, this field is optional

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updated 9.7 years ago by GenoMax

• written 9.7 years ago by Mehmet

According to their paper, the program should be able to download from here: https://prodege.jgi-psf.org/downloads/src

But the whole server seems to be down, I would suspect that is where the manual would be

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written 9.7 years ago by Tonor

I tried but I could not find anything about the program, including manual and program itself.

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written 9.7 years ago by Mehmet

Yeah the whole server seems to be down, the web version, the standalone version, the whole thing

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written 9.7 years ago by Tonor

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