Updating TODO

parent 04925ab4
......@@ -26,6 +26,14 @@ TODO list
-Allele frequency
2.5/ Produce the Textual output - December - Up to 12nd december:
-Add the strain presence files
3/ Automated labelling prediction (December) - After 12nd December
......@@ -38,14 +46,16 @@ TODO list
-bugwas bug
5/ Receive as input reads instead of contigs
5/ Show the strain presence for each node
6/ Show the strain presence for each node
-1st - just tabular export
-Search for JS libraries or use iTol
6/ Step1:
7/ Step1:
-Maf filter
-Remove nodes with a given AF
-Put in the docs that we count from genome assembly
......@@ -53,23 +63,23 @@ TODO list
7/ Textual output
-Add the strain presence files
8/ Step3:
9/ Step3:
-Layout with alongated nodes like Bandage
9/ Double-check SFF filter
10/ Double-check SFF filter
-When the 100th q-value is really not significant (like ~1), there is no meaning to generate a subgraph with the related unitigs.
The double check would be: take the top 100 q-values below a threshold (like the usual 0.05). Do you think we could try this ?
This would certainly lead to 2 different SFF parameters, which are somewhere correlated...
Integration with prokka
@see https://gitlab.com/leoisl/dbgwas/issues/8
Next release (v0.5.2 ETA 31/05/2018):
Continuous genotypes/phenotypes:
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