A High-Throughput and Extensible Toolkit for Processing FASTQ Data

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Documentation for package ‘fraq’ version 0.99.2

• 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)