Pear - Join Read Pairs

Join paired reads into single end reads based on sequence overlap

Location

  • Filepath: <SnakeLines_dir>/rules/paired_end/reads/preprocess/joined/pear.snake
  • Rule name: pear__join_read_pairs

Input(s):

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

Output(s):

  • r1: Left side of fragments without overlap in fastq format
  • r2: Right side of fragments without overlap in fastq format
  • rm: Paired reads with overlap joined into merged sequences in fastq format

Pear - Concat Joined With Single

Unite joined reads, and reads that could not be joined into a single fastq file. Sequence between reads without overlap would be filled with N symbol.

Location

  • Filepath: <SnakeLines_dir>/rules/paired_end/reads/preprocess/joined/pear.snake
  • Rule name: pear__concat_joined_with_single

Input(s):

  • r1: Left side of fragments without overlap in fastq format
  • r2: Right side of fragments without overlap in fastq format
  • rm: Paired reads with overlap joined into merged sequences in fastq format

Output(s):

  • rc: Concatenated file, first goes joined reads and then reads without overlap with N symbols between reads