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CAMI AMBER add length column (version 2.0.7+galaxy0)
Input a binning file in biobox format to generate a biobox format file with the extra column 'Length' which is needed for AMBER. Every other biobox format can be used for this as well!
Input the file which match to the gold standard file

What it does

This tool can create the gold standard file which has to be used for the CAMI AMBER.

Input

This tool required 2 inputs:

  • A binning file (biobox format)

This file can be created via the convert_to_biobox tool

Example(tab separated):

#CAMI Format for Binning
@Version:0.9.0
@SampleID:CAMI_low
@@SEQUENCEID   BINID
RL|S1|C10      Bin_034
RL|S1|C100     Bin_023
RL|S1|C1000    Bin_034
RL|S1|C10000   Bin_019
RL|S1|C10002   Bin_035
RL|S1|C10004   Bin_035
RL|S1|C10008   Bin_034
RL|S1|C10011   Bin_035
RL|S1|C10012   Bin_013
RL|S1|C10014   Bin_035
  • A fasta/fastq file (fasta,fasta.gz,fastq,fastq.gz format)

This file need the identical sequences which are in the gold standard file to create the finish gold standard file for CAMI AMBER

Output

As output the tool give you out a file in biobox format with the added column 'Length'. This file then can be used for AMBER as example!