Shouji: a fast and efficient pre-alignment filter for sequence alignment
...ocessing capacity of existing algorithms and compute infrastructures....e use of hardware/software co-design and hardware acceleration to sig...ly-costly dynamic programming algorithms. The first key idea of our p...boost the performance of our algorithm. More at https://github.c...1672 days ago
StringTie Transcript assembly and quantification for RNA-Seq
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algori...1454 days ago
alien_index : identify potential contaminants or horizontally transferred genes in transcriptomes.
identify potential contaminants or horizontally transferred genes in transcriptomes. algorithm is based on alogorithm described in the following: Gladyshev, Eugene A., Matthew Meselson, and Irina...1581 days ago
Musket - a multistage k-mer spectrum based corrector
Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and intro...1579 days ago
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies...1539 days ago
QuartataWeb: user-friendly server developed for polypharmacological and chemogenomics analyses.
Data on protein-drug and protein-chemical interactions are rapidly accumulating in data...; and many proteins bind chemicals other than those known, opening the way to design repurposable drugs, new chemi...1523 days ago
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from publ...our own data. Then they are fragmented and aligned to scaffolds using BWA mem algori...1479 days ago
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA...n microorganisms, as generated by contemporary metagenomics studies. The core algori...1476 days ago
1447 days ago
The wavefront alignment (WFA) algorithm
The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage ofhomologous regions between the sequences to ac...the alignment process. As opposed to traditional dynamic programming algori...1435 days ago