# A High-Throughput and Extensible Toolkit for Processing FASTQ Data

## Documentation for package ‘fraq’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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