List of software for creating simulated data sets

[w.lees]

A list of software developed to create simulated repertoires, either ab initio or using an existing repertoire as a base. See also https://goo.gl/oKGxLu which contains some additional details and was the base from which this list was created.

This is a wiki page. Please edit and add software you know about. However, note that this is not the place for closed-source commercial software vendors to advertise their products.

Tools that can be trained to mimic features of a given repertoire

• Igor (Marcou et al., 2017)
• Partis (Ralph and Matsen, 2016)
• repgenHMM (Elhanati et al., 2016)

Other related tools:

• AbSim (Yermanos et al., 2017)
• *Ig Simulator (Safonova et al., 2015)
• Igh Simulation (reported in Frost et al., 2015)

Tools that simulate mutations in an existing sequence or repertoire:

• SHazaM (Gupta et al., 2017) - introduces mutations into sequences or lineage trees, according to an SHM mutability/targeting model.

[steven.kleinstein]

Don’t forget SHMulate. Introduces mutations into sequences (shmulateSeq) or lineage trees (shmulateTree) according to a SHM mutability/targeting model, such as S5F. Implemented as part of the SHazaM package in the Immcantation suite. Method reported in (Gupta et al., 2017).

[w.lees]

Thanks Steve. I felt that it was best to introduce a third category for this and other related software. Feel free to edit or recategorise if you wish.