Results for "assembly"
Tags
What are the best method to validate genome assembly ?
I am working on a metazoan genome. I wanted to try the best known method to validate the assembly structure. Your suggestions are welcome.Tags: Genome, Assembly, Validation, Check
2249 days ago
What are the best software options available for nanopore (ONT) reads ?
Tags: ONT, Nanopore, Assembly, Sequencing, Reads, fast
2245 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
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 the initial assembly, Flye performs an extra repe...Tags: Flye, de novo, assembler, ONT, Nanopore, PacBio, Assembly, single, molecule, sequencing, reads
2245 days ago
- MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. The assembly process can be summarized as follows: overlap patch reads overlap (again) scrubbing assembly graph construction and touring o...
Tags: MARVEL, assembler, Assembly, Genome, ONT, Nanopore, PacBio
2245 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University, seehttp://arthropods.eugenes.org/EvidentialGene/Construction refers to the co...Tags: EvidentialGene, tr2aacds, mRNA, Transcript, Assembly, Software, Tools
2241 days ago
Installing Bandage on Ubunty !
The following instructions successfully build Bandage (https://github.com/rrwick/Bandage ) on a fresh installation of Ubuntu 14.04: Ensure the package lists are up-to-date: sudo apt-get update Install prerequisite packages: sudo apt-get install build-essential git qtbase5-dev libqt5...Tags: Install, Bandage, Ubuntu, Linux, Make, Tools, Genome, Assembly
2241 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available at: http://shendurelab.github.io/LACHESIS. Manusc...Tags: LACHESIS, Genome, Assembly, Hi-C, Contact, Probability, Maps, Genome, Assembly
2235 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to >1 megabase. This software, fragScaff, leverages...Tags: fragScaff, Genome, Assembly, Contiguity, Preserving, Transposition, Genome, Assembly
2235 days ago
GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this documentation, is distributed free of charge. If you u...Tags: GAPPadder, Sensitive, Approach, Closing, Gaps, Draft, Genomes, Short, Sequence, Reads, Genome, Assembly
2235 days ago
