SATSUMA : Highly sensitive whole-genome synteny alignments.
...rientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does not require any pre-processing, such as repeat masking, since it will automa...2877 days ago
Bioinformatics tools and software
...U sequences and improved diversity measures. UCHIME >Chimeric sequence detection. PILER >De novo genome repeat finder. PILER-CR >Detection of CRISPR repeats in bacterial genomes. Q...2823 days ago
2779 days ago
OPERA : Optimal Paired-End Read Assembler
...e local errors, improve efficiency etc.) and incorporated features that are important for scaffolding large genomes (multi-library support, better repeat-handling etc.), in addition t...2758 days ago
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FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads
FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.2586 days ago
Opera: An optimal genome scaffolding program
...large and complex genomes.Song Gao, Denis Bertrand, Burton K. H. Chia and Niranjan Nagarajan. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with...2313 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