Seal: SEquence ALignment evaluation suite
...ation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including: Reading a pre-...2307 days ago
LRCstats: Long Read Correction Statistics
...ne for benchmarking DNA long read correction algorithms for long reads outputted by t...in downstream analysis. Long read correction algorithms reduce the error rate of long...reads. Of course, some long read correction algorithms are better than others, and d...2305 days ago
PGAP-X: Extension on pan-genome analysis pipeline
PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize g...2287 days ago
2249 days ago
Metassembler: merging and optimizing de novo genome assemblies
...mblies into a combined consensus assembly using the best segments of the individual assemblies. Genome assembly projects typically run multiple algorithms in an attempt to find the sin...2182 days ago
HALC: High throughput algorithm for long read error correction
...HALC was able to obtain 6.7-41.1% higher throughput than the existing algorithms while maintaining comparable...thus result in 11.4-60.7% longer assembled contigs than the existing algorithms....2151 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
...ing, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient...2179 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
...e range of the read length. SOAPaligner benefitted in time and space efficiency by a revolution in the basic data structures and algorithms used.The core algorithms and the indexing data structu...2167 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.2166 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specif...2126 days ago