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Methyl-Seq

MethylFASTQ is a Python tool to simulate bisulfite sequencing data in a highly customizable way.

Features

MethylFASTQ produces two kind of files.

  • FASTQ file(s) that contains the sequenced reads. The id of each FASTQ record identifies the true mapping position of that read.
  • methylation call file that contains the true methylation call of each sequenced cytosine

It allows to simulate both whole genome bisulfite sequencing (WGBS) and targeted bisulfite sequencing experiments.

Options

  • -i fasta-file : path of the FASTA file containing the genome to be sequenced
  • -o output-file-path : directory where to save the artificial dataset
  • --seq {single_end,paired_end} : selected sequencing mode
  • --lib {directional,non_directional} : selected library mode
  • --chr chromosome-id [chromosome-id ...] : list of FASTA id of chromosomes to be sequenced
  • --regions target-regions : path of the .bed file containing chromosome regions to be sequenced
  • --coverage coverage : selected depth of coverage
  • --fragment fragment-size : size of produced fragments in fragmentation step
  • --read read-length : length of produced reads
  • --processes num-processes : maximum number of producer processes
  • --buffer buffer-size : buffer size of a single process
  • --cg CG-methylation-probability : probability that a C in CG context is methylated
  • --chg CHG-methylation-probability : probability that a C in CHG context is methylated (H = {A, C, T})
  • --chh CHH-methylation-probability : probability that a C in CHH context is methylated
  • --snp snp-probability : probability that a single nucleotide is a SNP (spontaneous mutation)
  • --error sequencing-error-probability : probability that a single nucleotide is a sequencing error
  • --maxq max-phred-score : maximum quality score in the produced reads
  • --minq min-phred-score : minimum phred score in the produced reads (not implemented yet)

Targeted sequencing

If you want to use targeted sequencing mode, you have to provide a region file describing the chromosome regions to be sequenced. The region file must be a TAB-delimited file with 3+ columns describing

  • the chromosome ID
  • the starting bp of the region to be sequenced
  • the last bp of the region to be sequenced

Check the region file in the example folder.