phcue-qc: a fast and simple summary of FASTQ files

Background

phcue-qc (pronounced fq qc) is a simple tool for summarizing FASTQ files for quality control purposes.

Running

phcue-qc [-t int] [-m int] <fastq-file> > <summary_text>

The required input:

• fastq-file: a FASTQ file, typically the R1 for paired-end sequencing where we would have fewer errors.

The options include:

• -t or --threads: the number of threads to use for parallelization.
• -m or --min-count: the minimum number of times a kmer must be observed to be included in the summary.

Get help:

phcue-qc -h

phcue-qc 0.2.0
A fast and simple summary of FASTQ.

USAGE:
    phcue-qc [OPTIONS] <input>

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
    -m, --min-count <min-count>     [default: 3]
    -t, --threads <threads>         [default: 1]

ARGS:
    <input>    Input file

Get the current version:

phcue-qc --version

The output

An example output:

Total reads: 636,311
Total bases: 160,520,099
Min read len: 35
Max read len: 301
Mean Q score: 36.09
Total kmers: 10,279,035
Total count: 147,771,738
Total unique: 4,807,539
Elapsed time: 6.555 seconds
Processing rate: 97072.62 reads/second