Pear - Join Read Pairs -------------------------- Join paired reads into single end reads based on sequence overlap **Location** - *Filepath:* /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:* /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