Hybrid assembly with Unicycler and multiple files of input

Question

[langziv]

Hello.
The input files I got are one of short reads - 89 contigs/scaffolds, and 107 fastq files of long reads. I need to concatenate the 107 files into one fastq, which then can be used as input?

[shelkmike]

Sorry, but your question is unclear. For example, "107 fastq files of long reads. I need to concatenate the 107 files into one fasta". FASTQ cannot be concatenated into FASTA. You probably mean something else.
If you want to concatenate FASTQ files, you can do this using the standard Linux command "cat". If you want to convert FASTQ to FASTA, you can use SeqKit (https://bioinf.shenwei.me/seqkit/usage/).

[langziv]

My question was if I should concatenate the FASTQ files in order to do hybrid assembly with Unicycler.

[shelkmike]

Yes, you should.