medaka: Sequence correction provided by ONT Research
...g data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on ba...1451 days ago
pggb: the pangenome graph builder
This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model). Its goal is to build a graph that is locally directed and...tion, and reuse of pangenome variation graphs....1333 days ago
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
...nomes sequenced so far. Hifiasm can produce primary/alternate assemblies of quality competitive with the best assemblers. It also introduces a new graph binning algorithm and achieve...1231 days ago
1190 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 haplo...using long reads and/or Hi-C data. As GraphUnzip only connects sequences...igs. To demonstrate the efficiency of GraphUnzip, we tested it on a simul...1188 days ago
JumboDB: tool for de Bruijn graph construction
jumboDB tool for fast de Bruijn graph construction from long sequences (reads or genomes) with very low err...r a subroutine that translates a set of reads into compressed de Bruijn graph. More at https://github...995 days ago
966 days ago
odgi: optimized dynamic genome/graph implementation
...and succinct dynamic DNA sequence graph model, as well as a host of a...orithms that allow the use of such graphs in bioinformatic analyses....rank in the global array of nodes. Graphs built from biological data s...n partially ordered regions of the graph, most deltas will require onl...827 days ago
Collection of Graph Visualization tools !
Standard approaches to genome inference and analysis relate sequences to a single linear reference genome. This is efficient but has a fundamental problem: Differences...470 days ago
98 days ago