SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-w...y. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson,...1530 days ago
1497 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
...assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembl...1462 days ago
medaka: Sequence correction provided by ONT Research
medaka is a tool to create a consensus sequence from nanopore sequencing data. T...pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on ba...1461 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....1343 days ago
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can...lies of quality competitive with the best assemblers. It also introduces a new graph binning algorithm and achieve...1241 days ago
1200 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...1198 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 erro...rather a subroutine that translates a set of reads into compressed de Bruijn graph. More at https://github...1005 days ago
976 days ago