1942 days ago
SvABA: Genome-wide detection of structural variants and indels 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,...1931 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 co...1918 days ago
Minipolish: A tool for Racon polishing of miniasm assemblies
Miniasm is a great long-read assembly tool: straight-...wever, it operates on FASTA files, not the GFA graphs that miniasm makes. Th...p a miniasm assembly, while keeping the assembly in graph form. It also takes care of...1616 days ago
NextDenovo: string graph-based de novo assembler for TGS long reads
NextDenovo is a string graph-based de novo assembler for TGS long...contains two core modules: NextCorrect and NextGraph. NextCorrect can be used to c...th approximately 15% sequencing errors, and NextGraph can be used to construct a st...1583 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
...Compiler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can b...number of false positive cycles. Our solution is to search the graph in multicores shared memory p...1560 days ago
1560 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
glia's main use is as a local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and producing an ordered stream of BAM...1560 days ago
Tadpole: an assembler, error-corrector, and read-extender
Tadpole is a kmer-based assembler, with additional capabilities of error-correcting and extending reads. It does not do any complicated graph analysis or scaffolding, and...1552 days ago
PANEV: an R package for a pathway-based network visualization
PANEV (PAthway NEtwork Visualizer) is an R package set for gene/pathway-based network...m 1 to n) of interconnected upstream and downstream pathways. The network graph visualization helps to interp...1547 days ago