2971 days ago
YASS :: genomic similarity search tool
...e transition constrained spaced seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA. Anoth...ckground frequencies parameterizable output filter for low complexity repeats reporting of various alignme...2887 days ago
Bioinformatics tools and software
...versity measures. UCHIME >Chimeric sequence detection. PILER >De novo genome repeat finder. PILER-CR >Detection of CRISPR repeats in bacterial genomes. QS...2823 days ago
2779 days ago
Laj: viewing and manipulating the output from pairwise alignment programs
...such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to othe...2584 days ago
NCBI Prokaryotic Genome Annotation Pipeline
...ing genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transpo...2508 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
Ultimate tool for resolving repeats in genome assemblies. Though the specific implementation of the idea of the rectangle graph approach is already included into the current SP...2282 days ago
RGFA: powerful and convenient handling of assembly graphs
...Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear pat...1529 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
...ssues which hinders from an adequate scaffolding evaluation are genome repeats. The previous standard for ev...Hunt et al., Genome Biology, 2014) did not take into account repeats. In this evaluation framework...2198 days ago
2123 days ago