Merging sequence files for metagenomics?

Question

[natrix36]

Hi everyone, i am new to Bioinformatics and I want to know if it is best to concatenate multiple fastq files into a single file using an R package before processing for bioinformatics analysis? Or is it best to do them separate.

Best wishes

[GenoMax]

This question is not clear so you may want to add some information about what you are trying to do. You have metagenomics tag so this is presumably such data.

There are standard pipelines to process most data types and they generally do not require concatenation (end to end joining) of data files. If your sample ran on multiple lanes of an Illumina flowcells (and you have lane specific files e.g. L001 etc in name) then such files could potentially be concatenated (in same order) for R1 and R2 (if you have paired-end data).