HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment...me). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original a...exing scheme is called a Hierarchical Graph FM index (HGFM). more...2216 days ago
MIX: Combining multiple assemblies from NGS data
Mix is a tool that combines two or more draft assemblies, w...nishing. The proposed algorithm builds an extension graph where vertices represent extr...put assembly corresponds to a path in the extension graph that maximizes the cumulative...2216 days ago
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TULIP - The Uncorrected Long read Integration Pipeline
TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. These...s as input alignments files of long reads to sparse short seeds, and outputs a graph and scaffold structures.2208 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex ps...h such structural feature. The bpRNA code is written in perl and requires the Graph perl module. Several addition...2201 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference...cies asm-to-asm alignment ./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf # PacBio read overl...2173 days ago
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ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short read...n constructs a novel data structure called red-black multipositional de Bruijn graph to detect misassemblies. In a...2157 days ago
FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
FMLRC, or FM-index Long Read Corrector, is a tool for perfo...d an FM-index and use that as an implicit de Bruijn graph. Each long read is then corre...ing high frequency k-mers in the implicit de Bruijn graph. In contrast to other de Brui...2121 days ago