MSAProbs - Parallel and accurate multiple sequence alignment
MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov...1789 days ago
Shouji: a fast and efficient pre-alignment filter for sequence alignment
...verwhelm the processing capacity of existing algorithms and compute infrastructures....r computationally-costly dynamic programming algorithms. The first key idea of our p...ures to further boost the performance of our algorithm. More at https://github.com/...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 algorithm as well as an optional de novo&nbs...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 Meselso...1582 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 appr...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 of genomes of...1539 days ago
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
...ic read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the packag...1480 days ago
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
...ome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gen...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 sequenc...gnment process. As opposed to traditional dynamic programming algorithms that run in quadratic time,...1435 days ago