Many-to-many pairwise alignments of two sequence sets
...or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum...algorithm uses a dynamic programming method to ensure the alignment is optimum, by exploring all...2141 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms t...2180 days ago
LAMSA: fast split read alignment with long approximate matches
...atches-based Split Aligner) is a novel split alignment approach with faster speed an...ors, and mitigate the effect of repeats. The alignments of the fragments are then us...sparse dynamic programming (SDP)-based split alignment approach to handle the large...2176 days ago
2168 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
...OAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short rea...2168 days ago
minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.2167 days ago
GenomeMapper: Simultaneous alignment of short reads against multiple genomes
GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align aga...2166 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...ref.fa reads.fa > aln.sam # Nanopore Direct RNA-seq ./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf # intra-species asm-to-asm alignment ./minimap2 -x ava-pb reads.f...2140 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
FastANI is developed for fast alignment-free computation of whole-genome Average Nuc...2007. However, it avoids expensive sequence alignments and uses Mashmap a...gine to compute the orthologous mappings and alignment identity estimates. Based on...2117 days ago
LSC :a long read error correction tool
...Cing! Latest publication Kin Fai Au, Jason Underwood, Lawrence Lee and Wing Hung Wong Improving PacBio Long Read Accuracy by Short Read Alignment [Manuscript] PLoS O...2097 days ago