Generalised Amplicon Coverage Analysis

[gordonkoehn]

The current amplicon coverage script devised by @dr-david won't work for all sets of primers and corresponding amplicons. The current logic exploits non-overlapping amplicon regions/positions to identify reads for a given amplicon.
This works already with already processed reads-per-position data.

If amplicons are arranged neatly to overlap each other this gets impossible. Then a more generalized rules are needed as for example: A given read belongs to a certain amplicon if it covers at least 50% of its bases. This requires the alignment of pre-processed reads with a tool like pySam, instead of the processed reads-per-position though.

[gordonkoehn]

Case 1: current implementation
Case 2: potential future implementation as environed by @DrYak

Generalized Amplivon Coverage Analyser_241016_154357 (1).pdf

[gordonkoehn]

To check whether a particular Amplicon Design is good, a test sequencing will be done, and the reads per amplicon are counted.
If we see that some amplicons do not have decent coverage, we may need to change the primer design.

In this group, we have scripts which do analyse the coverage – written by David – get Annika and Ivan think that they do not work on all sets of amplicons.

I shall investigate and if need be design a generalized version of an amplicon coverage script.

[gordonkoehn]

See for already existing software:

• https://github.com/erinyoung/ACI
• https://github.com/chienchi/amplicon_coverage_plot
• https://github.com/mgviz/amplicon_analysis

[gordonkoehn]

Next todo:

• chat with Annika
• chat with David
• check out the above packaged

[gordonkoehn]

• ask Adnan if they have something