How to Submit Methods to FAMES
Every member of the scientific community is welcome to submit their assembly/ gene prediction/ binning methods. The purpose of FAMeS it to provide an uniform platform for the evaluation and comparison of such methods.
If you wish to contribute your method for evaluation please follow the following guidelines
Download the corresponding data from the Download page
Run your method
Submit your results to FAMeS
Generate the files described in the next paragraphs and bundle them in a .zip or .rar or .tar.gz file and submit them.
In addition to the files described in the next paragraphs, please provide a file with a brief text describing your method or a link to a publication for your method
The results of the comparison of your method to the original genomes, and other methods in FAMeS will be available in a few hours
Submit an assembly method
Please provide a tab delimited files with the following columns:
[dataset] Should be any of : simLC,simMC,simHC.
[assembler] Should contain the name of the new method. Text is limited to 20 characters.
[contig_name] The name of the contig. Can contain alphanumeric characters and underscore but no spaces. Should not exceed 50 characters.
[read_name] The name of the read as found in the raw sequence data.
[read_strand] The strand of the read in the assembled contig (+ or -).
[contig_start] The left coordinates on the contig corresponding to the beginning of the read.
[contig_end] The right coordinates on the contig corresponding to the end of the read.
[read_start] The left coordinates of the read included in the contig (if not present 1 is assumed).
[read_end] The right coordinates of the read included in the contig (if not present the total length of the read is assumed).
If the assembler used produces scaffolds please provide a tab delimited file with the following columns:
[dataset]] Should be any of : simLC,simMC,simHC.
[assembler] Should contain the name of the new method. Text is limited to 20 characters.
[scaffold_name] The name of the scaffold. Can contain alphanumeric characters and underscore but no spaces. Should not exceed 50 characters.
[contig_name] The name of the contig belonging to this scaffold. Can contain alphanumeric characters and underscore but no spaces. Should not exceed 50 characters.
[contig_start] Starting coordinates of the contig on the scaffold.
[contig_end] Ending coordinates of the contig on the scaffold.
Provide a multi fasta file containing the sequence of the contigs.
Submit a gene prediction method
Please provide a tab delimited file with the following columns:
[dataset] should be any of : simLC,simMC,simHC.
[assembler] should be any of :Phrap,Arachne,JAZZ.
[gene prediction method] is a free text string shorter than 20 characters. Please do not include spaces in this field.
[gene ID] A unique identifier for the gene. Can contain any alphanumeric character, but no spaces, and should be shorter than 50.
[contig name] The name of the contig on which the gene was predicted. For assemblies that provide scaffolds please provide the scaffold names instead.
[gene start] The left coordinate of the gene on the contig or scaffold.
[gene end] The right coordinate of the gene on the contig or scaffold.
[strand] + or -.
Provide a multi fasta file containing the sequences of the genes. The header of each gene should be the gene ID
Submit a binning method
Please provide a tab delimited file with the following columns
[contig name] or [scaffold name] The name of the contig / scaffold (depending on the assembly method) that was binned.
[dataset] should be any of : simLC,simMC,simHC.
[assembler] should be any of :Phrap,Arachne,JAZZ.
[bin method] is a free text string shorter than 20 characters. Please do not include spaces in this field.
[bin name] corresponds to the name of a taxonomic group e.g. "Proteobacteria" or "Bacillales" etc. The name should be in accordance to the NCBI taxonomy nomenclature.
Check that you have prepared all the necessary files and
SUBMIT to FAMeS