Package: QuickBLAST 1.99.8

Vishvesh Karthik

QuickBLAST: High-Performance Sequence Alignment using BLAST and Apache Arrow

A BLAST Wrapper to call BLAST directly from R (interoperable and without Sys.call()) coupled with Apache Arrow's columnar format with parquet, IPC and csv file support.

Authors:Vishvesh Karthik [aut, cre, cph]

QuickBLAST_1.99.8.tar.gz
QuickBLAST_1.99.8.tar.gz(r-4.7-arm64)QuickBLAST_1.99.8.tar.gz(r-4.7-x86_64)QuickBLAST_1.99.8.tar.gz(r-4.6-arm64)QuickBLAST_1.99.8.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
QuickBLAST/json (API)

# Install 'QuickBLAST' in R:

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

Bug tracker:https://github.com/vizkidd/quickblast/issues

Uses libs:

libunwind– Library to determine the call-chain of a program
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

On CRAN:

software alignment sequencematching sequencing dataimport libunwind cpp openmp

4.02 score 23 exports 44 dependencies

Last updated from:4efe6de522. Checks:1 ERROR, 4 WARNING, 1 OK, 8 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	2517
linux-devel-arm64	WARNING	1587
linux-devel-x86_64	WARNING	2541
source / vignettes	OK	5044
linux-release-arm64	WARNING	1560
linux-release-x86_64	WARNING	2455
macos-release-arm64	FAIL	230
macos-release-x86_64	FAIL	343
macos-oldrel-arm64	FAIL	80
macos-oldrel-x86_64	FAIL	372
windows-devel	FAIL	5480
windows-release	FAIL	5471
windows-oldrel	FAIL	5495
wasm-release	FAIL	247

Exports:all2all BLAST1Folder BLAST2DBs BLAST2Files BLAST2Folders BLAST2Seqs BLASTFile2DB CreateQuickBLASTInstance DeleteQuickBLASTInstance GetAvailableBLASTOptions GetFASTAHeaders GetInstanceCount GetInstanceID GetQuickBLASTEnums GetQuickBLASTInstance GetQuickBLASTOptions isBLASTDB isQuickBLASTLoaded LoadBLASTHits MakeBLASTDB one2one RemoteBLAST SetQuickBLASTOptions

Dependencies:arrow assertthat BH bit bit64 callr cli codetools cpp11 digest dplyr fs future future.apply future.callr generics globals glue iterators lifecycle listenv magrittr otel parallelly pillar pkgconfig processx ps purrr R6 Rcpp RcppProgress RcppThread rlang stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs withr xfun

Exploring QuickBLAST

Rendered fromQuickBLAST.Rmdusingknitr::rmarkdown

Last update: 2026-07-21
Started: 2025-09-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get file path of file inside "bin" folder of package	.GetBinPath
Globals Get file path of file inside "libs" folder of package	.GetLibsPath
Execute all2all QuickBLAST	all2all
BLAST Files within a Folder	BLAST1Folder
BLAST 2 on-disk BLAST DBs	BLAST2DBs
BLAST 2 Files	BLAST2Files
BLAST 2 Folders	BLAST2Folders
BLAST 2 Sequence strings	BLAST2Seqs
BLAST File to a on-disk BLAST DB	BLASTFile2DB
Create new QuickBLAST instance with seq_type, strand, program and BLAST options.	CreateQuickBLASTInstance
Delete a QuickBLAST instance stored in C++ side	DeleteQuickBLASTInstance
Get a List of Available BLAST options	GetAvailableBLASTOptions
Get FASTA Headers	GetFASTAHeaders
Get count of QuickBLAST instances stored in C++ side	GetInstanceCount
Get ID/Index of a QuickBLAST instance stored in C++ side	GetInstanceID
Get a list of Enums used by QuickBLAST	GetQuickBLASTEnums
Get QuickBLAST instance stored in C++ side at ID/Index	GetQuickBLASTInstance
Get BLAST options for a QuickBLAST instance as a string.	GetQuickBLASTOptions
Check BLAST DB Files	isBLASTDB
Check R <-> C++ (FFI) connection	isQuickBLASTLoaded
Load BLAST Hits into a data.frame	LoadBLASTHits
Make on-disk BLAST DB from a FASTA file	MakeBLASTDB
Execute one2one QuickBLAST	one2one
BLAST query against remote NCBI DBs	RemoteBLAST
Set BLAST options for a QuickBLAST instance.	SetQuickBLASTOptions