Package: fraq 1.1.1

Travers Ching

fraq: A High-Throughput and Extensible Toolkit for Processing FASTQ Data

High-throughput extensible toolkit for processing FASTQ data. The goal of this package is to empower users to quickly build out small programmatic 'kernels' to define any FASTQ processing task they may need. Builds on Intel TBB’s flow graph to orchestrate concurrent I/O and data processing; throughput can be as fast as compression and disk speed allows. The package also ships with a suite of predefined kernels for common FASTQ tasks.

Authors:Travers Ching [aut, cre, cph], Yann Collet [ctb, cph], Facebook, Inc. [cph], Reichardt Tino [ctb, cph], Skibinski Przemyslaw [ctb, cph], Mori Yuta [ctb, cph]

fraq_1.1.1.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fraq/json (API)

# Install 'fraq' in R:

install.packages('fraq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/traversc/fraq/issues

Uses libs:

libzstd– Fast lossless compression algorithm
c++– GNU Standard C++ Library v3

On BioConductor:fraq-1.1.1(bioc 3.24)fraq-1.0.0(bioc 3.23)

software infrastructure sequencing dnaseq qualitycontrol alignment libzstd cpp

4.38 score 1 stars 12 scripts 22 exports 20 dependencies

Last updated from:d482adc4a8. Checks:1 NOTE, 12 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	221
linux-devel-arm64	OK	259
linux-devel-x86_64	OK	296
source / vignettes	OK	285
linux-release-arm64	OK	256
linux-release-x86_64	OK	316
macos-release-arm64	OK	201
macos-release-x86_64	OK	325
macos-oldrel-arm64	OK	158
macos-oldrel-x86_64	OK	363
windows-devel	OK	249
windows-release	OK	241
windows-oldrel	OK	268
wasm-release	FAIL	190

Exports:fraq_align fraq_chunk fraq_concat fraq_convert fraq_count_barcodes fraq_demux fraq_downsample fraq_export_shortreadq fraq_fifo_supported fraq_import_shortreadq fraq_mem_list fraq_mem_load fraq_mem_remove fraq_merge_pairs fraq_options fraq_quality_filter fraq_rcpp_template fraq_run_r fraq_slice fraq_summary fraq_trim_adapters generate_random_fastq

Dependencies:BiocGenerics Biostrings cli crayon edlibR generics glue IRanges lifecycle magrittr Rcpp RcppParallel rlang S4Vectors Seqinfo stringfish stringi stringr vctrs XVector

fraq: A high-throughput extensible toolkit for processing fastq data

Rendered fromfraq_getting_started.Rmdusingknitr::rmarkdown

Last update: 2026-05-03
Started: 2025-11-13

Help page	Topics
Align a query to a target	fraq_align
Chunk sequencing files into fixed-size batches	fraq_chunk
Concatenate sequencing files	fraq_concat
Convert sequencing files between supported formats	fraq_convert
Count barcodes in FASTQ file(s)	fraq_count_barcodes
Demultiplex FASTQ file(s) by barcode prefix	fraq_demux
Downsample FASTQ file(s)	fraq_downsample
Detect FRAQ FIFO support	fraq_fifo_supported
Manage in-memory FASTQ datasets	fraq_mem_list fraq_mem_load fraq_mem_remove
Merge paired-end reads into a consensus	fraq_merge_pairs
Get or set FRAQ options	fraq_options
Filter reads by whole-read quality	fraq_quality_filter
Generate an example fraq Rcpp script	fraq_rcpp_template
Run an R kernel over sequencing reads	fraq_run_r
Bridge FRAQ formats with ShortReadQ	fraq_export_shortreadq fraq_import_shortreadq fraq_shortread
Slice reads by index or limit	fraq_slice
Summarize FASTQ quality metrics (single- or paired-end)	fraq_summary
Trim adapters from FASTQ file(s)	fraq_trim_adapters
Generate a random FASTQ file (optionally gzipped)	generate_random_fastq

Package: fraq 1.1.1

fraq: A High-Throughput and Extensible Toolkit for Processing FASTQ Data

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Help Manual

Usage by other packages (reverse dependencies)