Recombination Test
With the emergence of recombinant ASFV of genotype I and genotype II, we use recombination_test.py to quickly identify whether an ASFV genome is recombinant and what its recombination pattern is.
recombination_test.py
Description
We generated consensus CDS sequences from genotype I and II isolates. The CDS predicted from input ASFV genome using Prodigal were compared to consensus sequences using BLASTN (e-value 1e-5). Output a table indicating whether each CDS is closer to genotype I or genotype II.
Input
An ASFV genome file (fasta format).
Example
recombination_test.py single_fasta/OQ504956.1.fasta > OQ504956.1_recombination_test.tsv
Output
A 6-column tsv table, the 6 fields are CDS name, Start, End, Similarity with GenotypeI, Similarity with GenotypeII and Conclusion. The following table is a partial example of a recombinant
| CDS | Start | End | GenotypeI | GenotypeII | Conclusion |
|---|---|---|---|---|---|
| F165R | 54963 | 55373 | 100 | 97.567 | I |
| F1055L | 55360 | 58527 | 99.937 | 97.277 | I |
| K205R | 58696 | 59313 | 100 | 97.896 | I |
| K78R | 59402 | 59638 | 99.578 | 100 | II |
| K196R | 59635 | 60225 | 98.816 | 100 | II |
| K145R | 60241 | 60678 | 98.63 | 100 | II |
| K421R | 60712 | 61980 | 98.503 | 100 | II |
| EP1242L | 62021 | 65749 | 99.142 | 98.713 | I |
| EP84R | 65828 | 66082 | 99.608 | 95.686 | I |
| EP424R | 66118 | 67377 | 97.536 | 98.73 | II |
| EP152R | 67872 | 68330 | 97.386 | 100 | II |
recombination_plot.py
Description
Use the table generated by recombination_test.py as input and draw a graph to show the recombination pattern.
Input
tsv table generated by recombination_test.py
Arguments
| Argument name | Required | Description |
|---|---|---|
| -f, --format | No | output format (jpg, png or pdf, default=pdf) |
Example
recombination_plot.py OQ504956.1_recombination_test.tsv
Output
A circular genome map.
The following plot is an example of a recombinant:
