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With awk..

awk '{ for(i=1;i<=NF;i++){ print $i}}' file > new_file

$ xargs -n1 < file
@HWI-ST212
1:N:0
AGTCCTACCGGGAGT
+
@@@DDDDDHHHHHII
@HWI-ST212
1:N:0
CGTTTAAAAATTTCT
+
@;@B;DDDDH?:F;F
@HWI-ST212
1:N:0
TCGGAGATTCCGTAC
+
???DDDDDDDDDDII
@HWI-ST212...