Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
...**experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can be...1617 days ago
1617 days ago
Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg) Link to working demo: https://vgteam.github.io/sequenceTubeMap/1574 days ago
pggb: the pangenome graph builder
...preserving large-scale variation. Maintaining local linearity is important for the interpretation, visualization, and reuse of pangenome variation graphs....1388 days ago
GraphUnzip: Phases an assembly graph using Hi-C data and/or long reads.
GraphUnzip, a fast, memory-efficient and accurate tool to unzip assembly graphs into their constituent haplotypes using long reads and/or Hi-C data. As GraphUnzip only connects sequen...1243 days ago
k-mers tutorial - classification and taxonomy
DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lot of time thinking about how to store k-mer graphs efficiently, discard redund...1041 days ago
odgi: optimized dynamic genome/graph implementation
...graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. C...where the node id corresponds to the rank in the global array of nodes. Graphs built from biological data se...881 days ago
MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly
...housands of records. The indexing workflow always follows the same principle, transforming single input samples into error-removed, refined sample graphs, which are then merged into a...24 days ago
Panacus : A Counting Tool for Pangenome Graphs
panacus is a tool for calculating statistics for GFA files. It supports GFA files with P and W lines, but requires that the graph is&...18 days ago