Hi All,
I am a newbie to sequencing technologies. 

Is there a way to quantify the paired-end sequencing overlap. since completely overlapping the read pairs would be a waste of sequencing resources. A bit of overlap can be useful when doing the alignment but a small gap is optimal to maximize coverage.

Is there a way to check sequencing efficiency by using the alignment files. Because if there is lots of overlap we want to improve this.

Any help is appreciated.

Thank you.
Yes, you can do this with alignment BAM/SAM file. You can extract the record for concordant alignment `YT:Z:CP` from SAM/BAM file. Once you have concordant alignment, you can look for field 9 in SAM/BAM file. Field 9 (9th column) represents the fragment length of paired-end sequences.

From here, you can get the fragment length distribution. Based on your sequencing protocol, you should have the insert size for paired-end sequences. Then you should compare the fragment length with the insert size. If the fragment length is less than the sum of two reads, it means your paired sequences are overlapped. Here, you can plot the histogram of fragment length distribution.

Note: concordant alignment record will give you the alignments which are within the given insert size