Produce a basic 2 column table with sample name and results/comments.
For example, for a fully sequenced AIV genome:
All 8 segments were sequenced. Predicted subtype is H5N1. Top HA BLAST match is Influenza A virus (A/place/xx/2020) (NCBI accession). Top NA BLAST match is Influenza A virus (A/place/xx/2020) (NCBI accession).
or for a partially sequenced AIV genome:
Only 7 segments were sequenced and assembled. The NA segment could not be assembled due to lack of reads (N=5). Predicted subtype was H5 with undetermined N subtype. Top HA BLAST match is Influenza A virus (A/place/xx/2020) (NCBI accession).
TODO
[ ] handle multiple cases of various gene segments missing or low coverage
[ ] mixed sample reporting
[ ] report depth and breadth of coverage of segments below thresholds
Produce a basic 2 column table with sample name and results/comments.
For example, for a fully sequenced AIV genome:
or for a partially sequenced AIV genome:
TODO