is there function used in alignment on fastq file , or using alignment tools is better ? and what is the tool or function to do that ?
Ehm, you'll need to explain a bit more what you are doing, but I'm 99% sure you need an alignment tool and R is not appropriate for your project.
You pretty much said what I wanted to write :)
sot exactly what you said is true, i have DNA_sqe on big fastq size, and have another sequence want to be alignment it with the sequences in the fastq file .... so what pacjages can use in R to do the alignment process?
Are you really limited to using just R? Do you only have a Windows OS?
R is tailoured for downstream data analysis due to limits in its very architecture, mainly in terms of memory. R has recently acquired many functions that are parallel-process enabled, though.
It is possible to make system calls from R but these then still require non-R programs to do alignment.
Take a look at this old thread (and I agree wholeheartedly with Devon and Sean): NGS DNA-seq analysis packages for mapping, calling cariants, annotation on R / bioconductor
The only R package I am aware of is Rsubread https://bioconductor.org/packages/release/bioc/html/Rsubread.html
But the best tool for your project is likely not accessible through R.
Use alignment tools - there are various aligners - bwa, bowtie, BBMap.
bwa, bowtie, BBMap. > what are those ? are they R packages!!
They are non-R, compiled programs that require UNIX, linux, or MAC. They perform re-alignment of FASTQ / FASTA files to a reference genome.