HipSTR: Haplotype inference and phasing for Short Tandem Repeats
HipSTR was specifically developed to deal with these errors in the hopes of obt...by: Learning locus-specific PCR stutter models using an EM algorithm Mining candidate STR alleles from po...1925 days ago
Minipolish: A tool for Racon polishing of miniasm assemblies
Miniasm is a great long-read assembly tool: straight-forward, effective and very 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...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 long reads. It u...novo contains two core modules: NextCorrect and NextGraph. NextCorrect can be used to c...s with approximately 15% sequencing errors, and NextGraph...1622 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
Reference free SNP search for comparative population genomics: multiple samples run sim...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...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...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 visualization. Based on info...m 1 to n) of interconnected upstream and downstream pathways. The network graph...1586 days ago
SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph...1557 days ago
1523 days ago