Minipolish: A tool for Racon polishing of miniasm assemblies
...r long-read data. However, it operates on FASTA files, not the GFA graphs that miniasm makes. Th...se Racon to polish up a miniasm assembly, while keeping the assembly in graph form. It also takes care of...1607 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...1574 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
...ler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can b...ve number of false positive cycles. Our solution is to search the graph in multicores shared memory p...1551 days ago
1551 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...1551 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 therefore,...1543 days ago
PANEV: an R package for a pathway-based network visualization
...n KEGG, it visualizes genes within a network of multiple levels (from 1 to n) of interconnected upstream and downstream pathways. The network graph visualization helps to interp...1538 days ago
SvABA: Structural variation and indel detection by local assembly
...ructural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson,...1509 days ago
1476 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
...mbler, 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...1441 days ago