Software Tools


Hybrid De Novo Assembler (HyDA)

HyDA is a multipurpose assembler, particularly tested for single cell and normal multicell genome co-assembly. HyDA source code is released under GNU GPL ver3 here.


Squeezamler is a divide-and-conquer algorithm for economical sequencing and assembly of all distinct genomes in a bacterial sample. The key idea here is exploiting sparsity, which is the small number of distinct genomes (~1000) in comparison to the huge number of cells (~100 trillion). Squeezambler source code as well as sample datasets are released here. Ensemble analysis of different divide-and-conquer strategies is released here.

Velvet for Single Cells

Velvet-SC is an adaptation of Velvet assembler for single cell genome assembly. For superior results, it is recommended to use HyDA instead of Velvet-SC. However, if you decide to use Velvet-SC, we recommend using Camel error correction before assembly. Velvet-SC can be downloaded locally as well.

Partition function of Interacting RNAs (piRNA)

piRNA is an open source toolbox to calculate RNA-RNA interaction partition function, base pairing probabilities, equilibrium concentrations, and melting temperature.

Binding sites of Interacting RNAs (biRNA)

biRNA is a fast open source tool based on a heuristic algorithm to compute RNA-RNA binding sites.

RNA Newton Polytope

The Matlab code for the 2D (#AU, #CG) and 3D (#AU, #CG, #GU) RNA Newton polytope and verification of the necessary condition for learnability of energy parameters can be found here.