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.2228 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...2227 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
...o assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome...2188 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...idering those reads which should assemble together. Reducing/removing reference bias as compared to mapping based approaches. The software is designed to work in situations where a...2165 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
...urity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read seque...2151 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
...stitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produ...2080 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...orithms that address these shortcomings have the potential to achieve better and more accurate integration of these two technologies. Results: We designed and developed Hercules, the f...2140 days ago
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