Description

Perform adapter and quality trimming on sequencing reads with reporting

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

List of input FastQ files of size 1 and 2 for
single-end and paired-end data, respectively.

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

reads (file)

The trimmed/modified fastq reads

*trimmed.fastq.gz

reads_fail (file)

Reads that failed the preprocessing (Optional with —discard args setting)

*discard.fastq.gz

reads_unpaired (file)

Reads without matching mates in paired-end files (Optional)

*trimmed.unpaired.fastq.gz

stats (file)

trimming/qc text stats file

*.stats.txt

debug (directory)

trimming/qc files from —debug option

./debug

statspdf (file)

trimming/qc pdf report file

*_qc_report.pdf

log (file)

fastq log file

*.log
maintainers
Github user mjcipriano
Github user sateeshperi
Github user hseabolt
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

faqcs
GPLv3 License

FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.

github.com/LANL-Bioinformatics/FaQCs 10.1186/s12859-014-0366-2