Crate fasten_trim

Blunt-end trims using 0-based coordinates

Examples

Trim five bases from the right side

cat file.fastq | fasten_trim -l -5 > trimmed.fastq

Keep a maximum of 100bp

cat file.fastq | fasten_trim -l 99 > trimmed.fastq

Trim 5bp from the left side

cat file.fastq | fasten_trim -f 4  > trimmed.fastq

Usage

Usage: fasten_trim [-h] [-n INT] [-p] [-v] [-f INT] [-l INT]
 
Options:
    -h, --help          Print this help menu.
    -n, --numcpus INT   Number of CPUs (default: 1)
    -p, --paired-end    The input reads are interleaved paired-end
    -v, --verbose       Print more status messages
    -f, --first-base INT
                        The first base to keep (default: 0)
    -l, --last-base INT The last base to keep. If negative, counts from the
                        right. (default: 0)

Functions

• main 🔒
• trim_worker 🔒
  Trim a set of fastq entries and send it to a channel