BioStar
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ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
By Rahul Nayak 3000 days agofaculty.cse.tamu.edu - 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 specifically designed for performing transcriptome assembly from...HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
By Jit 3049 days agogithub.com - HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2726 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2632 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
By Abhimanyu Singh 3406 days agogithub.com - GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which...ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole...
By Rahul Nayak 3000 days agogithub.com - ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 2329 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...The Genome 10K Project
By Jit 4435 days agohttps://genome10k.soe.ucsc.edu The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction...SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
By Abhimanyu Singh 3406 days agoufmg-simba.sourceforge.net - SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS)...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Jit 3059 days agogithub.com - Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After...
