Tags: MEGAHIT, ultra-fast, single-node, solution, large, complex, metagenomics, assembly, succinct, de Bruijn, graph
1998 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 acyclic while preserving large-scale variation. Maintaining local linearity is important for the interpreta...Tags: pggb, pangenome, graph, builder
1328 days ago
wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. ./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo p...Tags: wtdbg2, fuzzy, Bruijn, graph, approach, long, noisy, reads, assembly
1916 days ago
Tags: VG, variation, graph, structures, interchange, formats, alignment, genotyping, variant, calling, methods, snp
1558 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 sequences in the assembly graph that already had a potential link based on overlaps, it yields high-quality gap-less sup...Tags: GraphUnzip, Phases, assembly, graph, Hi-C, data, long reads
1183 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 error rate. JumboDB is not a genome assembler by itself but rather a subroutine that translates a set of reads into compressed de Bruijn graph. More at https://github.com/AntonBankevich/j...Tags: JumboDB, tool, de Bruijn, graph, construction
991 days ago
odgi: optimized dynamic genome/graph implementation
odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. Careful encoding of graph entities allows odgi to efficiently compute and transform pangenomes with mini...Tags: odgi, optimized, dynamic, genome, graph, implementation, genome, assembly, graph
822 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 from this reference are hard to observe and describe in a coherent way. Variation and sequence are separated. https://fu...Tags: graph, map, vg, plot
465 days ago
Tags: GraphPath, graph, model, pathway-pathway, interaction, network
37 days ago