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...1957 days ago
Minipolish: A tool for Racon polishing of miniasm assemblies
Miniasm is a great long-read assembly tool: straight-f...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...1655 days ago
NextDenovo: string graph-based de novo assembler for TGS long reads
NextDenovo is a string graph-based de novo assembler for TGS l...core modules: NextCorrect and NextGraph. NextCorrect can be us...ely 15% sequencing errors, and NextGraph can be used to construct a st...re sensitive and accurate dovetail overlaps, and some useful utilities...1622 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
Reference free SNP search for comparative population genomi...meration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can b...ositive cycles. Our solution is to search the graph in multicores shared memory p...1599 days ago
1599 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...1599 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...1591 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...1586 days ago
SvABA: Structural variation and indel detection by local assembly
...r the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, an...y Heng Li. Contigs are assembled for every 25kb window (with some small overlap) for every region in the ge...1557 days ago
1539 days ago