quack

A FASTQ quality assessment tool

Citation

A. Thrash, M. Arick, and D. G. Peterson, “Quack: A quality assurance tool for high throughput sequence data,” Analytical Biochemistry, vol. 548, pp. 38–43, 2018. https://doi.org/10.1016/j.ab.2018.01.028

Latest Release

The latest release of quack and its binaries can always be found here.

Dependencies

zlib
klib (pulled by the submodule update below)

Installation from Source

git clone https://github.com/IGBB/quack.git

cd quack/

make && make test

Binaries

Binaries are available in the bin/ folder. Current testing of these binaries has been limited. If a binary doesn't work, try compiling from source on your system.

Running Quack

Quack has the following options.

  -1, --forward     forward strand data in gzipped FASTQ format, must be used with -2 or --reverse
  -2, --reverse     reverse strand data in gzipped FASTQ format, must be used with -1 or --forward
  -a, --adapters    adapters in gzipped FASTA format (optional)
  -n, --name    a descriptive name to be printed with the output image (optional)
  -u, --unpaired    unpaired data in gzipped FASTQ format
  -?, --help, --usage   prints the help or usage information
  -V, --version prints the program version

Quack takes gzipped FASTQ-formatted files as input for data and gzipped As output, quack prints an SVG formatted image to standard output.

Examples

Paired-end with name and adapters

quack -1 reads.1.fastq.gz -2 reads.2.fastq.gz -n sample_name -a adapters_files.fasta.gz > sample_name.svg

Unpaired with name and adapters

quack -u reads.fastq.gz -n sample_name -a adapters.fa.gz > sample_name.svg

Paired-end without name and adapters

quack -1 reads.1.fastq.gz -2 reads.2.fastq.gz > sample_name.svg

Unpaired without name and adapters

quack -u reads.fastq.gz > sample_name.svg

Output

Quack is capable of producing output for single-ended data and paired-end data. Only the singled-ended data is labeled, since the paried-end data has all the same parts.

Single-ended Data

explanation

A. The base content distribution showing the percentage of each nucleotide in each column of an array.
B. A heatmap showing the distribution of sequence quality for each column and a line representing mean quality scores across the array
C. A score distribution graph showing the percentage of bases matching certain scores, with 100% on the left of the graph and 0% on the right. The highest scoring data appears at the top of the graph.
D. Length distribution graph showing the percentage of reads of a given length
E. Adapter content distribution graph showing how adapter content is distributed throughout an array

Paired-end Data

paired

IGBB / quack

readme