Package: fraq 1.0.0
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:
fraq_1.0.0.tar.gz
fraq_1.0.0.zip(r-4.7)fraq_1.0.0.zip(r-4.6)fraq_1.0.0.zip(r-4.5)
fraq_1.0.0.tgz(r-4.6-x86_64)fraq_1.0.0.tgz(r-4.6-arm64)fraq_1.0.0.tgz(r-4.5-x86_64)fraq_1.0.0.tgz(r-4.5-arm64)
fraq_1.0.0.tar.gz(r-4.7-arm64)fraq_1.0.0.tar.gz(r-4.7-x86_64)fraq_1.0.0.tar.gz(r-4.6-arm64)fraq_1.0.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
fraq/json (API)
NEWS
| # Install 'fraq' in R: |
| install.packages('fraq', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/traversc/fraq/issues
On BioConductor:fraq-1.1.1(bioc 3.24)fraq-1.0.0(bioc 3.23)
softwareinfrastructuresequencingdnaseqqualitycontrolalignmentcpp
Last updated from:014474668c (on RELEASE_3_23). Checks:1 NOTE, 12 OK, 1 FAIL. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 207 | ||
| linux-devel-arm64 | OK | 347 | ||
| linux-devel-x86_64 | OK | 414 | ||
| source / vignettes | OK | 311 | ||
| linux-release-arm64 | OK | 319 | ||
| linux-release-x86_64 | OK | 399 | ||
| macos-release-arm64 | OK | 294 | ||
| macos-release-x86_64 | OK | 544 | ||
| macos-oldrel-arm64 | OK | 285 | ||
| macos-oldrel-x86_64 | OK | 443 | ||
| windows-devel | OK | 377 | ||
| windows-release | OK | 373 | ||
| windows-oldrel | OK | 401 | ||
| wasm-release | FAIL | 138 |
Exports:fraq_alignfraq_chunkfraq_concatfraq_convertfraq_count_barcodesfraq_demuxfraq_downsamplefraq_export_shortreadqfraq_fifo_supportedfraq_import_shortreadqfraq_mem_listfraq_mem_loadfraq_mem_removefraq_merge_pairsfraq_optionsfraq_quality_filterfraq_rcpp_templatefraq_slicefraq_summaryfraq_trim_adaptersgenerate_random_fastq
Dependencies:abindBHBiobaseBiocGenericsBiocParallelBiostringsbitopscigarilloclicodetoolscpp11crayonDelayedArraydeldiredlibRformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluehwriterinterpIRangesjpeglambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatspngpwalignRColorBrewerRcppRcppEigenRcppParallelRhtslibrlangRsamtoolsS4ArraysS4VectorsSeqinfoShortReadsnowSparseArraystringfishstringistringrSummarizedExperimentvctrsXVector
Readme and manuals
Help Manual
| 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 |
| 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 |
