Trimmomatic - Trim ReadsΒΆ

Remove low quality ends of reads and then filter reads that are too short.

Location

  • Filepath: <SnakeLines_dir>/rules/paired_end/reads/preprocess/trimmed/trimmomatic.snake
  • Rule name: trimmomatic__trim_reads

Input(s):

  • r1: Left side of sequenced fragments in gzipped fastq format
  • r2: Right side of sequenced fragments in gzipped fastq format

Output(s):

  • r1: Left side of subsampled fragments without overlap in gzipped fastq format
  • r2: Right side of subsampled fragments without overlap in gzipped fastq format