With BBMap suite:
reformat.sh in=your.fq.gz out=filtered.fq.gz minlength=N
Set N
to a reasonable number (very short reads are not useful anyway). Set to 1
if you just want to remove empty reads.
With BBMap suite:
reformat.sh in=your.fq.gz out=filtered.fq.gz minlength=N
Set N
to a reasonable number (very short reads are not useful anyway). Set to 1
if you just want to remove empty reads.