Crate fasten_validate

Validates your reads and makes you feel good about yourself!

Examples

Quick validation with stderr message

cat file.fastq | fasten_validate --verbose

Validate that your reads are paired end

cat R1.fastq R2.fastq | fasten_shuffle | fasten_validate --paired-end

Parallelize

Large-scale validation of PE reads with 4 CPUs and xargs

\ls *_1.fastq.gz | xargs -n 1 -P 4 bash -c '
  echo -n "." >&2 # progress bar
  R1=$0
  R2=${0/_1.fastq.gz/_2.fastq.gz}
  zcat $R1 $R2 | fasten_shuffle | fasten_validate --paired-end
'

Usage

    Usage: fasten_validate [-h] [-n INT] [-p] [-v] [--min-length INT] [--min-quality FLOAT] [--paired-end] [--print-reads] [-v]
     
    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
            --min-length INT
                            Minimum read length allowed
            --min-quality FLOAT
                            Minimum quality allowed
            --paired-end    The reads are interleaved paired-end
            --print-reads   Print the reads as they are being validated (useful
                            for unix pipes)

Functions

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