fuse fastq files with multiple records
Based on the comments of the question I thought to put together this answer using GNU coreutils which should exist on pretty much all systems.

The idea is to paste the 2 files together with paste (assuming they are in the same order and each line correspond to the same line in the other file).

Since only the sequence and quality of both files should be kept, the lines starting with @ and + need to be made empty for one of the files. This can be achived with sed, e.g. sed 's/^@.*//' empties all lines starting with @ but keeps the empty line.

To modify the second file on the fly, one can using process substitution &lt;(). 
Everything strung together should be something like this:

file1=File_A.fastq
file2=File_B.fastq
paste -d "" $file1 &lt;(cat $file2 | sed 's/^@.*//' | sed 's/^+.*//') &gt; target.fastq


I haven't tested it thoroughly, but could be a good starting point.

If you have a lot of files to paste, you might however want to process them first (not on the fly) using:

for file in $(ls *.fastq); do 
  cat $file | sed 's/^@.*//' | sed 's/^+.*//' &gt; ${file%.fastq}_cleaned.fastq
done


This creates File_A_mod.fastq from File_A.fastq etc. 
Best to move them in a separate directory (make sure the first one is the original instead of the _cleaned one since it serves as the base).
You should have the following in the folder: File_A.fastq File_B_cleaned.fastq File_C_cleaned.fastq .... 
Those can be than pasted with paste -d "" *.fastq &gt; target.fastq.