HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies
HyPo is a HYbrid POlisher that utilises short as well as long reads within a single run to polish a long reads assembly of small and large genomes. Hypo generates significantly more accurate polished assembly in about one-third time with about half the memory requirements in comparison to contemporary widely used polishers like Racon.
SUPBUB: Superbubbles
SUPBUB is a tool that, in linear time, finds out superbubbles (special subgraph-structures) in a directed graph. It is being used in the vg (variation graph) toolkit developed by Richard Durbin’s lab at the Wellcome Trust Sanger Institute.
Suk: Solid (Unique) Kmers Module
SUK is a C++ module (library and stand-alone tool) for finding Solid (Unique) Kmers from genomic reads data.
SLOG: Simple LOGging library
Slog is a simple C++ library for logging timing and memory (Max RSS) usage.
ElDeS: Elastic-Degenerate Strings
ElDeS is a tool that finds out occurrences of degenerate patterns in an elastic-degenerate text.
lspf: Longest Successor and/or Previous Factor Array
lspf is a tool to compute the longest previous and/or successor factor array/s of a given string in linear time.
ClusteredClumps
ClusteredClumps is a tool that finds out clustered-clumps of : degenerate patterns in a solid text; solid patterns in a degenerate text; and degenerate patterns in a degenerate text.
APDS: Approximate Patter-matching in Degenerate Strings
APDS is a tool that finds out (in linear time) approximate occurrences of a degenerate pattern in a given input sequence.
degLPF: Longest Previous Factor (LPF) Array in a Degenerate String
degLPF is a tool that computes the LPF (Longest Previous Factor) Array for a given degenerate sequence. Currently it takes only the files mimicking FASTA format.
WebSlate
WebSlate is a language/environment to create slides which are displayable in a web-browser. The language syntax is LATEX-inspired and compiles down to HTML/CSS/JS. Elm , a new functional reactive programming language has been used for development.