FAVITES

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I should add new `NodeEvolution` and `SequenceEvolution` modules for SANTA-SIM: * Paper: https://academic.oup.com/ve/article/5/1/vez003/5372481?login=true * Tool: https://github.com/santa-dev/santa-sim

niemasd

I should add a new `Sequencing` module(s) for ReSeq, which seems to have more realism than ART for simulating Illumina reads: * Paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02265-7 * Tool: https://github.com/schmeing/ReSeq

niemasd

Does not properly identify seed nodes

2

## FAVITES Version 1.2.0 ## Environment Docker ## Configuration File [toy_SAPHIRE.json.zip](https://github.com/niemasd/FAVITES/files/5013262/toy_SAPHIRE.json.zip) ## Unexpected Behavior I set up 20000 nodes fro the contact network, 1 seed "P" node, and 19999 susceptible...

pekarj

Create transmission module implementations for EoN: https://epidemicsonnetworks.readthedocs.io/en/latest/

niemasd

Similar to Seq-Gen, πBUSS is a sequence evolution tool. - Website: https://rega.kuleuven.be/cev/ecv/software/pibuss - Paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-133

niemasd

Add random number generator seed functionality

1

Need to figure out how to make it work on every single random function and external tool

niemasd