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