Package: Rfastp 1.17.0

Thomas Carroll

Rfastp: An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).

Rfastp is an R wrapper of fastp developed in c++. fastp performs quality control for fastq files. including low quality bases trimming, polyX trimming, adapter auto-detection and trimming, paired-end reads merging, UMI sequence/id handling. Rfastp can concatenate multiple files into one file (like shell command cat) and accept multiple files as input.

Authors:Wei Wang [aut], Ji-Dung Luo [ctb], Thomas Carroll [cre, aut]

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Rfastp.pdf |Rfastp.html✨
Rfastp/json (API)

# Install 'Rfastp' in R:
install.packages('Rfastp', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3

On BioConductor:Rfastp-1.17.0(bioc 3.21)Rfastp-1.16.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

qualitycontrolsequencingpreprocessingsoftwarezlibcpp

3.82 score 33 scripts 301 downloads 5 exports 36 dependencies

Last updated 2 months agofrom:041105867a. Checks:OK: 1 NOTE: 4 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-win-x86_64NOTENov 30 2024
R-4.5-linux-x86_64NOTENov 30 2024
R-4.4-win-x86_64NOTENov 30 2024
R-4.4-mac-x86_64WARNINGNov 30 2024
R-4.4-mac-aarch64WARNINGNov 30 2024
R-4.3-win-x86_64NOTENov 30 2024
R-4.3-mac-x86_64WARNINGNov 30 2024
R-4.3-mac-aarch64WARNINGNov 30 2024

Exports:catfastqcurvePlotqcSummaryrfastptrimSummary

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2Rhtslibrjsonrlangscalesstringistringrtibbleutf8vctrsviridisLitewithrzlibbioc

An Ultra-Fast All-in-One FASTQ preprocessor

Wei Wang [email protected]

Rendered fromRfastp.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2020-10-01
Started: 2020-06-18