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ReadsClassifier.md

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Reads classifier tools are provided to compare two metagenomes. Algorithm splits reads from one metagenome based on their presence in de Bruijn graph built from other metagenome.

Usage example

Simple reads classifier

Simple reads classifier splits reads into two categories.

Here is a bash script showing a typical usage of simple reads classifier:

java -jar metacherchant.jar --tool reads-classifier \
    -k 31 \
    -i <input_1.fasta input_2.fasta> \
    -r <reads_1.fasta reads_2.fasta> \
    -found 90 \
    -w <workDir> \
    -o <outDir>
  • -k --- the size of k-mer used in de Bruijn graph.
  • -i --- two files with paired reads for de Bruijn graph. FASTA and FASTQ formats are supported, as well as compressed files *.gz or *.bz2.
  • -r --- two files with paired reads to be classified. FASTA and FASTQ formats are supported, as well as compressed files *.gz or *.bz2.
  • -found --- Minimum coverage breadth for reads from class found [0 - 100 %].
  • -w --- directory with intermediate working files
  • -o --- directory for final categories of reads

Output description

After the end of the analysis, the results can be found in the folder specified in -o parameter

  • found_[1|2|s].fastq --- reads which were found in de Bruijn graph built from input reads

  • not_found_[1|2|s].fastq --- reads which were not found in de Bruijn graph built from input reads

Triple reads classifier

Triple reads classifier splits reads into three categories. It utilizes two values of k and several heuristic thresholds (can be user defined) for more accurate classification.

Here is a bash script showing a typical usage of triple reads classifier:

java -jar metacherchant.jar --tool triple-reads-classifier \
    -k 31 \
    -k2 61 \
    -i <input_1.fasta input_2.fasta>
    -r <reads_1.fasta reads_2.fasta>
    -found 90 \
    -half 40 \
    -w <workDir> \
    -o <outDir>
  • -k --- the size of k-mer used in de Bruijn graph.
  • -k2 --- the second size of k-mer used in de Bruijn graph. k2 > k
  • -i --- two files with paired reads for de Bruijn graph. FASTA and FASTQ formats are supported, as well as compressed files *.gz or *.bz2.
  • -r --- two files with paired reads to be classified. FASTA and FASTQ formats are supported, as well as compressed files *.gz or *.bz2.
  • -found --- Minimum coverage breadth for reads from class found [0 - 100 %].
  • -half --- Minimum coverage breadth for reads from class half-found [0 - 100 %].
  • -w --- directory with intermediate working files
  • -o --- directory for final categories of reads

Output description

After the end of the analysis, the results can be found in the folder specified in -o parameter

  • found_[1|2|s].fastq --- reads which were found in de Bruijn graph built from input reads

  • half_found_[1|2|s].fastq --- reads which were partially found in de Bruijn graph built from input reads

  • not_found_[1|2|s].fastq --- reads which were not found in de Bruijn graph built from input reads