FASTA/FASTQ have 1 entry per sequenced read, such that a paired-end sequenced fragment will have two entries (usually in different files)
SAM/BAM files have 1 entry per read alignment, such that a paired-end sequenced fragment can have 1, 2, or 3+ entries.
Is there a format that is just 1 entry per fragment? Can contain alignment info or not.
Thanks very much :)